Manual¶
Basic usage¶
Getting started¶
Given an existing sequence alignment in a file data.dat in FASTA format,
the simplest usage might be:
mview -in fasta data.dat
Similarly, if the input file contained a CLUSTAL alignment:
mview -in clustal data.dat
In either case, the output would be a stacked alignment with extra columns added to show row numbers and percent coverage and percent identity (with respect to the first sequence, see Coverage and identity), looking something like this, regardless of the input format:
Reference sequence (1): EGFR_HUMAN
Identities normalised by aligned length.
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
To process the output of a BLAST run use something like:
mview -in blast blastresults.dat
while to process the output of a FASTA run (the sequence database search program from U. of Virginia, not the simple FASTA/Pearson data format) use something like:
mview -in uvfasta fastaresults.dat
The -in option isn’t always necessary. If the filename extension, or the
filename itself minus any directory path begins with or contains the first few
letters of the valid -in options (e.g., mydata.msf or mydata.fasta
or tfastx_run.dat), MView tries to choose a sensible input format,
allowing multiple files in mixed formats to be supplied on the command
line. The -in option will always override this mechanism but requires that
all input files be of the same format.
The ruler line¶
The ruler line at the top is enabled by default. To remove it, use the
-ruler off option:
mview -in fasta -ruler off data.dat
gives:
Reference sequence (1): EGFR_HUMAN Identities normalised by aligned length. 1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC 2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV 3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC 4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC 5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Removing the ruler also removes some column header information, which could cause confusion.
Only one kind of ruler is currently provided, numbering the columns of the final alignment from M to N (incrementing) or N to M (decrementing) based on the input sequence numbering, if any. For multiple alignments like the one above with no numbering the ruler runs from 1 to the length of the alignment.
For database searches that translate nucleotide sequences to protein, such as TBLASTX, the rulers differ slightly in that the native query numbering is given in nucleotide units, but MView reports amino acid units instead (using modulo 3 arithmetic).
Command line options¶
ALl available options can be listed using:
mview -help
There are a lot of options, but the main ones are described in this manual.
Many of them can be abbreviated as long as they are unambiguous, for example,
the option -reference can be shortened to -ref.
Layout and filtering¶
Pagination¶
The default layout is a single unbroken horizontal band of alignment - fine if
scrolling inside Firefox. However, you may prefer to break the alignment into
vertically stacked panes. For panes, for example, 80 columns wide, set
-width 80. Widths refer to the alignment, not to the whole displayed
output.
Column ranges¶
It is possible to narrow (or expand) the displayed range of columns of the
alignment, for example, -range 10:78 would select only that column range
using the numbering scheme reported when -ruler on is set (see
The ruler line). Note: the range setting is not related to the sequence
position labelling for blast/fasta database search input; it’s just the
position along the ruler.
The order of the numbers is unimportant making it simpler to state interest in a region of the alignment that might actually be reversed in the output (e.g., a BLASTN search hit matching the reverse complement of the query strand).
Changing the reference sequence¶
One can colour and compute identities with respect to a sequence other than
the first/query sequence using the -reference option.
This takes either the sequence identifier or an integer argument corresponding to the ranking or ordering of a sequence usually shown in the first labelling column of MView output. For multiple alignment input formats, sequences are numbered from 1, while for searches the hits are numbered from 1, but the query itself is 0, so beware.
Sorting by percent coverage or percent identity¶
By default MView outputs sequences in the same order they were read in and computes percent coverage and percent identity values (see Coverage and identity).
You can change the ordering with the -sort option:
-sort cov
-sort pid
-sort cov:pid
-sort pid:cov
to sort the output (descending) by coverage, percent identity, coverage then percent identity, or percent identity then coverage. Rows that coincide in the sort retain their original local ordering (ascending row number).
You can also change the reference sequence (see Changing the reference sequence) and apply one of these sorts like this:
-ref 2 -sort cov:pid
which would compute all the coverage and percent identities with respect to row 2, then sort by coverage and percent identity placing row 2 first.
Default ordering taken from the input alignment:
Reference sequence (1): EGFR_HUMAN Identities normalised by aligned length. 1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC 2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV 3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC 4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC 5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
After sorting by coverage and percent identity to row 2:
Reference sequence (2): PR2_DROME Identities normalised by aligned length. 2 PR2_DROME 100.0% 100.0% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV 1 EGFR_HUMAN 100.0% 35.7% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC 5 KIN31_CAEEL 100.0% 30.1% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA 4 PTK7_HUMAN 97.1% 25.0% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC 3 ITK_HUMAN 92.6% 33.8% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
Filtering rows¶
Showing only the top N rows
Usually, specifying a limited number of hits to view from a long search
alignment speeds things up a lot as there’s less parsing and less formatting
to be generated, so to get the best 10 hits, use the option -top 10.
Filtering by percent identity
The -minident N option will report only those hits above some threshold
percent identity N compared to the reference row; useful for looking for close
matches to the query or other reference sequence.
Similarly, you can exclude the strong matches using -maxident N.
Both options can be combined.
Showing and hiding sets of rows
Rows can be dropped explicitly using the -hide option. This can be
supplied a comma-separated list of row identifiers, rank numbers, rank number
ranges (1,2,3, 1..3, 1:3 are all equivalent), regular expressions (case
insensitive, enclosed between // characters) to match against row identifiers,
or the * symbol meaning all rows.
Likewise, the -show option specifies a list of rows to keep in the
alignment. The -show option overrides -hide whenever a row is common
to both.
For example, the options:
-hide all -show '2,3,6..10,/^pdb/'
or even:
-hide '/.*/' -show '2,3,6:10,/^pdb/'
would hide everything except rows 2, 3, 6 through 10 inclusive, and any hits beginning with the string ‘pdb’.
Note: the currently set reference row is still used for percent identity and
colouring operations, even though the row may have been dropped from display
by the -hide list (see Changing the reference sequence).
Data format specific filters
Other filters specific to BLASTP, FASTA, etc., input formats allow cutoffs on
scores or p-values, etc. In particular, it is possible to apply some control
over the selection of HSPs used in building the MView alignment using the
-hsp filtering option.
Some search programs produce DNA strand-directional output (e.g., BLASTN) and you can extract or output the results separately. For example, to see just the plus strand matches:
mview -in blast -strand p blastn_results.dat
The choices are p, m, both.
Of interest to anyone using PSI-BLAST, you can display alignments for any/all iterations of a PSI-BLAST run using, say:
mview -in blast -cycle 1,last psiblast_results.dat
to get just those two iterations. The default is to display only the last
iteration. If you want all output, use -cycle all.
Keeping rows, but ignoring them in calculations
Another control option can be used to prevent MView from using rows for
colouring or for calculation of percent identities although these rows will
still be displayed. Use -nop to specify a list (comma-separated as usual)
of identifiers or row numbers to flag for “NO Processing”.
Comment lines, another way to ignore rows
If a sequence identifier starts with the # character, it is treated as a
nop row, i.e., as a comment. This is useful for displaying other textual
information (e.g., secondary structure predictions) within the alignment.
Here is an example with two lines of input data beginning with dummy
identifiers #residues and #properties:
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
residues ------------------------------------------^Lys--------------^Glu----------------
properties ------------------------------------^^^^^^hydrophobic---------------------------
Note 1: MView elides the hash character in the output and also the row numbers. However, the name or row number based filtering mechanism described above still works.
Note 2: Comment lines like this cannot contain whitespace in the sequence region - they look like sequences and are processed as such by MView.
Labels, annotations and sequences¶
You can switch off some of the displayed columns, referred to here as labels. Labels are in blocks numbered from zero (perverse, but the original reasoning was that the input data starts with the sequence identifiers in column 1 and MView tacks on a rank number in front, so make that column 0).
Column
Description
0
rank
1
identifier
2
description
3
score block (may contain many score columns)
4
percent coverage
5
percent identity
6
query sequence positions (blast or fasta searches)
7
hit sequence positions (blast or fasta searches)
8
trailing optional fields (blast -outfmt 7 data)
Any of the of the label types can be switched off with an option like
-label2 to remove the descriptions label at column 2, and so on.
You can also disable processing and display of the sequences with the
-sequences off option. This would be useful if you only want to see
summarized scoring information from many blast runs, for example.
Adding HTML¶
Basic HTML¶
To add some HTML markup a few extra options are needed, for example:
mview -in fasta -html head data.dat > data.html
produces a complete page of HTML and you can load this into your Web browser
with a URL like file:///full/path/to/the/folder/data.html.
To colour all the residues using the default built-in colourmap for proteins:
mview -in fasta -html head -coloring any data.dat > data.html
produces:
Reference sequence (1): EGFR_HUMAN
Identities normalised by aligned length.
Colored by: property
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
To make the letters stand out use the -bold option:
mview -in fasta -html head -bold -coloring any data.dat > data.html
giving:
Reference sequence (1): EGFR_HUMAN Identities normalised by aligned length. Colored by: property 1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC 2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV 3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC 4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC 5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Or change the colouring to use blocked letters with -css on instead:
mview -in fasta -html head -css on -coloring any data.dat > data.html
giving:
Reference sequence (1): EGFR_HUMAN
Identities normalised by aligned length.
Colored by: property
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
You can combine -css on with -bold to make the blocks and letters even
more prominent.
If your data are DNA or RNA, add the option -moltype dna (or rna or
na for “nucleic acid”) to change to the default nucleotide
colourmap. Here’s an MView run on some BLASTN data demonstrating some other
options as well:
mview -in blast -html head -css on -coloring identity -moltype dna -top 5 -range 250:310 blastn.dat
which (slightly edited to reduce space) produced:
HSP processing: ranked
Query orientation: +
cov pid query sbjct 250 [ . . . . 3 ] 310
EMBOSS_001 bits E-value N qy ht 100.0% 100.0% 1:521 TGAAGCCTGCACTTACTCAGGACTCATCATGACTGCGTACCAATTCGTCTTACTCAGGACT
1 EM_EST:GT222018.2 1033 0.0 1 + + 100.0% 100.0% 1:521 4:524 TGAAGCCTGCACTTACTCAGGACTCATCATGACTGCGTACCAATTCGTCTTACTCAGGACT
2 EM_EST:GT222017.1 186 4e-43 1 + + 88.5% 98.2% 256:372 205:318 ------CTGCACTTACTCAGGACTCATCATGACTGCGTACCAATTCGT-TTACTCAGGACT
3 EM_EST:GT222024.2 182 7e-42 1 + + 80.3% 100.0% 262:372 96:209 ------------TTACTCAGGACTCATCATGACTGCGTACCAATTCGTCttACTCAGGACT
4 EM_EST:GT222023.2 182 7e-42 1 + + 80.3% 100.0% 262:372 96:209 ------------TTACTCAGGACTCATCATGACTGCGTACCAATTCGTCttACTCAGGACT
5 EM_EST:GT222054.2 178 1e-40 1 + + 52.5% 100.0% 279:372 4:97 -----------------------------TGACTGCGTACCAATTCGTCTTACTCAGGACT
showing scoring and sequence range information parsed from the BLASTN run, and using the default nucleotide colouring scheme (purines, dark blue; pyrimidines, light blue). Notice the lower-cased pairs of thymines near the end of sequences 3 and 4, columns 299–300 indicating where a segment of hit sequence has been excised to close a gap in the query (see Why are some sequence symbols lowercased?).
Controlling the amount of HTML¶
There are several values that can be passed to the -html option: head,
body, data, full, off.
Mode head
Produces a complete web page. Output includes the style sheet if -css on
was given. The most common situation.
Mode body
Produces just the <BODY></BODY> part of the web page. Note: the style
sheet produced by -css on will be missing.
Mode data
Produces just the alignment part of the web page. Note: any style sheet
produced by -css on will be missing.
Mode full
Produces a complete web page with the MIME-type "text/html", suitable for
serving directly from a web server. Output includes the style sheet if -css
on was given.
Mode off
Switches off HTML (default).
Using an external CSS style sheet¶
The option -listcss dumps the style sheet to stdout, so you can share that
across MView invocations from a web server. Each would be of the form:
mview -css URL
where the URL specifies the location of the style sheet as seen by the web
server (i.e., file:///some/path or http://server/path).
If you build a new colourmap you can load it into MView and save the new CSS
file. Suppose you have a new colourmap in newcolmap.dat:
mview -colorfile newcolmap.dat -listcss
will dump the new style sheet for use as before.
Consensus sequences¶
Clustal conservation line¶
A Clustal-style conservation line of *:. symbols can be added to any
alignment (not just one from CLUSTAL itself) using the -conservation on
option:
mview ... -conservation on
giving:
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
clustal . : :* * ** * . **:* .: * .* .:.: : :: .:
The symbols are * for full column identity, and : or . for strong
and weak amino acid grouping, respectively, as defined in CLUSTAL.
For DNA or RNA sequences, if the molecule type was set to nucleic acid with
-moltype na or dna or rna, then the clustal conservation line will
show only the column identities.
Note: these conservation lines can be generated for any subset of rows extracted using the various row filtering options (see Filtering rows).
Consensus lines¶
Consensus lines can be added beneath the alignment using -consensus on. By
default, this adds four extra lines of consensus sequences computed at various
thresholds of percentage composition of the columns.
There are default consensus patterns for protein and nucleotide (either DNA or RNA) sequences. MView starts up with the default protein consensus pattern, for example:
mview ... -consensus on
gives:
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
consensus/100% hp..p.lG.GtFG.V..u.h...................VAlKphp.t........ph.cEh.hM.plpp.plsphhuls
consensus/90% hp..p.lG.GtFG.V..u.h...................VAlKphp.t........ph.cEh.hM.plpp.plsphhuls
consensus/80% lphsKplGsGtFGhVhhGhhhs..............hh.VAlKpl+.ts.s....p-hhcEAtlMtplpH.plVpLhGls
consensus/70% lphsKplGsGtFGhVhhGhhhs..............hh.VAlKpl+.ts.s....p-hhcEAtlMtplpH.plVpLhGls
Changing consensus thresholds¶
The default consensus mechanism displays consensus lines calculated at four
levels of identity (100%, 90%, 80%, 70%). This can be changed to show as many
or as few consensus lines at any level of percent identity between 50 and 100%
using the -con_threshold option and a comma-separated list of identities:
mview ... -consensus on -con_threshold 80
would give a single consensus line calculated at 80% identity, while:
mview ... -consensus on -con_threshold 80,65
would produce two lines at 80% and 65% identity.
Consensus pattern definitions¶
Consensus patterns are based on equivalence classes, that is, sets of residues that share some predefined property. These classes are not mutually exclusive and the consensus mechanism will choose the most specific class that summarizes a given column at the desired percent identity.
The default for protein alignments is called P1 and is defined by
physicochemical property as follows:
[P1] #Protein consensus: conserved physicochemical classes, derived from #the Venn diagrams of: Taylor W. R. (1986). The classification of amino acid #conservation. J. Theor. Biol. 119:205-218. #description => symbol members . => . A => A { A } C => C { C } D => D { D } E => E { E } F => F { F } G => G { G } H => H { H } I => I { I } K => K { K } L => L { L } M => M { M } N => N { N } P => P { P } Q => Q { Q } R => R { R } S => S { S } T => T { T } V => V { V } W => W { W } Y => Y { Y } alcohol => o { S, T } aliphatic => l { I, L, V } aromatic => a { F, H, W, Y } charged => c { D, E, H, K, R } hydrophobic => h { A, C, F, G, H, I, K, L, M, R, T, V, W, Y } negative => - { D, E } polar => p { C, D, E, H, K, N, Q, R, S, T } positive => + { H, K, R } small => s { A, C, D, G, N, P, S, T, V } tiny => u { A, G, S } turnlike => t { A, C, D, E, G, H, K, N, Q, R, S, T } stop => * { * }
The default nucleotide consensus pattern is D1 grouping bases by ring type
(purine, pyrimidine). It is selected when any of the nucleotide molecule types
is set -moltype na (for “nucleic acid”; also dna or rna), for
example:
mview ... -consensus on -moltype dna
and has the following definition:
[D1] #DNA consensus: conserved ring types #Ambiguous base R is purine: A or G #Ambiguous base Y is pyrimidine: C or T or U #description => symbol members . => . A => A { A } C => C { C } G => G { G } T => T { T } U => U { U } purine => r { A, G, R } pyrimidine => y { C, T, U, Y }
Changing consensus patterns¶
The available list of built-in patterns can be seen with -listgroups.
Alternative equivalence classes can be selected using -con_groupmap. For
example, to select the CYS built-in consensus pattern to show only
conserved cysteines you would use an invocation like:
mview ... -consensus on -con_groupmap CYS
New groups can be defined in the same format and read in from a file using
the -groupfile option.
Showing conserved residues or conserved classes¶
Two options -con_ignore and -con_gaps can be used to tune the
consensus lines. Consider the following alignment:
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
The default consensus pattern for proteins, with these options:
mview ... -consensus on -con_threshold 80
would add this consensus line:
consensus/80% lphsKplGsGtFGhVhhGhhhs..............hh.VAlKpl+.ts.s....p-hhcEAtlMtplpH.plVpLhGls
comprising a mixture of conserved residue classes and residues, whichever is more specific.
If you just want to see the conserved physicochemical classes, use -con_ignore singleton:
consensus/80% lphs+plusutauhlhhuhhhs..............hh.lul+pl+.ts.s....p-hhc-utlhtplp+.pllplhuls
Alternatively, to see just the conserved residues, use -con_ignore class:
consensus/80% ....K..G.G.FG.V..G.....................VA.K.................EA..M....H...V.L.G..
Lastly, the default consensus computation counts gap characters in each
column, so that gapped regions are diluted and may not show up in the
consensus. Building on the last example, setting -con_gaps off prevents
this:
consensus/80% ....K..G.G.FG.V..G........LPKGSMN......VA.K.........E.......EA..M....H...V.L.G..
The consensus sequence now runs the full length of the alignment because the insert in sequence 4 spanning the gap has been added to the consensus. This is a little contrived in this case, but is sometimes useful when you want to preserve as much of the alignment as possible.
These options work similarly with nucleotide alignments and with any other consensus pattern you choose.
Note: it is possible to colour the consensus sequences independently of the alignment (see Consensus pattern colouring).
Colouring modes¶
Alignment colouring¶
There are several basic ways to colour the alignment using the -coloring
option which takes five modes: any, identity, mismatch,
consensus, group. These all have default associated colour schemes,
but you can supply a different one or just a single colour by name (see the
description for the mismatch mode for an example).
Mode any
The simplest is to colour every residue according to the currently selected colourmap:
mview -html head -css on -coloring any
gives:
Colored by: property
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Mode identity
You can colour only those residues that are identical to some reference sequence (usually the query or first row) with:
mview ... -coloring identity
to produce:
Colored by: identity
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
or with respect to another row (let’s use row 4):
mview ... -coloring identity -ref 4
giving:
Colored by: identity
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 87.2% 21.2% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 84.6% 25.0% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 80.8% 26.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 100.0% 100.0% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 91.0% 22.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
in which also you see that the percent identity calculations have been recomputed with respect to the new row of interest.
Mode mismatch
Behaves like identity mode, but colours only those residues that differ
from the reference sequence (the query or first row unless specified
otherwise) with:
mview ... -coloring mismatch
to produce:
Colored by: mismatch
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Using a single colour
That’s using the default protein colourmap and rather difficult to see, so let’s mark all mismatched residues in red:
mview ... -coloring mismatch -colormap red
to produce:
Colored by: mismatch
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
This approach of using a single colour works with any of the colouring modes
listed above. To see colours and colormaps use mview -listcolors.
You can add new colours or build your own multicoloured specialist colourmap. For example, you might want certain important mismatched residues showing up in one colour against a ground colour of all the other mismatches (see Colours).
Mode consensus
This mode uses the currently selected alignment colourmap to colour only those
residues assigned to a consensus class for each column (see
Consensus sequences). The consensus threshold defaults to 70% and
and may be set to another value with the -threshold option. In the
following example we add a single consensus line and set the same threshold
for both consensus calculations (they are independent) to 90%:
mview ... -coloring consensus -threshold 90 -consensus on -con_threshold 90
gives:
Colored by: consensus/90%
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
consensus/90% hp..p.lG.GtFG.V..u.h...................VAlKphp.t........ph.cEh.hM.plpp.plsphhuls
Notice that the coloured columns correspond to the consensus features (i.e., not wildcards or gaps). In each column, the residues that contribute to that consensus class have been coloured using the prevailing alignment colourmap (see Alignment colouring), which is the default one used in the other examples in this section.
Mode group
The last mode works like the consensus colouring mode, but gives the residues in a column a uniform colour defined for that consensus class (see Consensus pattern colouring):
mview ... -coloring group -threshold 90 -consensus on -con_threshold 90
yields:
Colored by: consensus group/90%
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
consensus/90% hp..p.lG.GtFG.V..u.h...................VAlKphp.t........ph.cEh.hM.plpp.plsphhuls
As in the last example, the coloured columns correspond to the consensus features (i.e., not wildcards or gaps). In each column, the residues that contribute to that consensus class have been coloured using a single colour defined for that consensus class (see Consensus pattern colouring), and conserved residues (at least 90% of a column) are given a solid coloured background for emphasis.
The choice of consensus classes may be changed using the -groupmap name
option, where name is the name of a consensus pattern. These can be listed
using the -listgroups option (see Changing consensus patterns).
Note: it is also possible to colour the consensus sequences themselves independently of the alignment (see Consensus pattern colouring).
Conserved residue colouring¶
The colouring of an alignment under the consensus or group colouring
modes (see Alignment colouring) can be tuned to ignore the
consensus classes with -ignore class for the purposes of colouring:
mview ... -coloring group -threshold 90 -consensus on -con_threshold 90 -ignore class
gives:
Colored by: consensus group/90%
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
consensus/90% hp..p.lG.GtFG.V..u.h...................VAlKphp.t........ph.cEh.hM.plpp.plsphhuls
which highlights the conserved residues (at least 90% of a column) in the alignment by applying the default consensus group colouring scheme to them.
Finding and colouring motifs¶
Occurrences of a string or pattern defined by a regular expression can be
coloured using the -find 'pattern' option. This will cause all instances
of the pattern to be highlighted using the user selected colourmap. Patterns
are case-insensitive.
Exact strings
mview ... -html head -css on -find VAIK
Colored by: search pattern 'VAIK'
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Regular expressions
Regular expressions containing any of the shell metacharacters in the set [
] { } ( ) | ^ $ ? * must be enclosed in quotes. This example finds V A
followed by either I or V then K:
mview ... -find 'VA[IV]K'
Colored by: search pattern 'VA[IV]K'
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Patterns can span gaps in the sequence
The pattern (any 5 residues followed by V A) has intact instances in the last two rows, but also spans a gap in the first three rows:
mview ... -find '.{5}VA'
Colored by: search pattern '.{5}VA'
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Patterns find the longest match
Patterns are greedy and try to find the longest possible match. This looks for a subsequence starting with by V and ending with G:
mview ... -find 'V.*G'
Colored by: search pattern 'V.*G'
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Alternative patterns
Alternative patterns separated by | characters receive the same colouring:
mview ... -find 'VAIK|VAVK|[LI]G.G|[DKER]E[AI]..M|[VIL]V[QR]L'
Colored by: search pattern 'VAIK|VAVK|[LI]G.G|[DKER]E[AI]..M|[VIL]V[QR]L'
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Alternative patterns with different colours
Alternative patterns separated by : characters receive a different colouring:
mview ... -find 'VAIK:VAVK:[LI]G.G:[DKER]E[AI]..M:[VIL]V[QR]L'
Colored by: search pattern 'VAIK:VAVK:[LI]G.G:[DKER]E[AI]..M:[VIL]V[QR]L'
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Note: if you specify more patterns than the number of colours available (currently 20) the colours are cycled.
Combining both types of alternative pattern
Patterns containing both | and : are allowed, with | taking
precedence. That is, all neighbouring patterns separated by | are treated
as one colour group, and groups separated by : are given different
colours:
mview ... -find 'VAIK|VAVK|[LI]G.G:[DKER]E[AI]..M|[VIL]V[QR]L'
Colored by: search pattern 'VAIK|VAVK|[LI]G.G:[DKER]E[AI]..M|[VIL]V[QR]L'
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Combining alignment and motif colouring¶
It is possible to combine the alignment colouring mode with a motif search. For example, this shows mismatches to the query in a light grey overlaid with two coloured motifs:
mview ... -coloring mismatch -colormap gray5 -find 'G.G.FG.V:VA.K'
Colored by: mismatch; search pattern 'G.G.FG.V:VA.K'
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
Consensus pattern colouring¶
The consensus lines may be coloured independently of the alignment. The
--con_coloring option takes two modes: any, identity.
Mode any
The simplest is to colour every consensus symbol according to the currently selected consensus colourmap:
mview ... -consensus on -con_coloring any
gives:
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
consensus/100% hp..p.lG.GtFG.V..u.h...................VAlKphp.t........ph.cEh.hM.plpp.plsphhuls
consensus/90% hp..p.lG.GtFG.V..u.h...................VAlKphp.t........ph.cEh.hM.plpp.plsphhuls
consensus/80% lphsKplGsGtFGhVhhGhhhs..............hh.VAlKpl+.ts.s....p-hhcEAtlMtplpH.plVpLhGls
consensus/70% lphsKplGsGtFGhVhhGhhhs..............hh.VAlKpl+.ts.s....p-hhcEAtlMtplpH.plVpLhGls
Alternative colourmaps can be set using the -con_colormap option. In
particular, a predefined uniform colour can be chosen:
mview ... -consensus on -con_coloring any -con_colormap brown
gives:
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
consensus/100% hp..p.lG.GtFG.V..u.h...................VAlKphp.t........ph.cEh.hM.plpp.plsphhuls
consensus/90% hp..p.lG.GtFG.V..u.h...................VAlKphp.t........ph.cEh.hM.plpp.plsphhuls
consensus/80% lphsKplGsGtFGhVhhGhhhs..............hh.VAlKpl+.ts.s....p-hhcEAtlMtplpH.plVpLhGls
consensus/70% lphsKplGsGtFGhVhhGhhhs..............hh.VAlKpl+.ts.s....p-hhcEAtlMtplpH.plVpLhGls
Mode identity
Instead of colouring all the consensus symbols, we can just colour those that are identical to the reference sequence. Here we colour the consensus identities with respect to the first alignment row:
mview ... -consensus on -con_coloring identity
gives:
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
consensus/100% hp..p.lG.GtFG.V..u.h...................VAlKphp.t........ph.cEh.hM.plpp.plsphhuls
consensus/90% hp..p.lG.GtFG.V..u.h...................VAlKphp.t........ph.cEh.hM.plpp.plsphhuls
consensus/80% lphsKplGsGtFGhVhhGhhhs..............hh.VAlKpl+.ts.s....p-hhcEAtlMtplpH.plVpLhGls
consensus/70% lphsKplGsGtFGhVhhGhhhs..............hh.VAlKpl+.ts.s....p-hhcEAtlMtplpH.plVpLhGls
These modes work with the -con_gaps and -con_ignore options in various
combinations to tune the consensus symbols displayed (see
Showing conserved residues or conserved classes).
Make consensus span low coverage regions
The strict consensus calculation can be relaxed to ignore gaps, so that the consensus is also computed across lower coverage regions:
mview ... -consensus on -con_coloring any -con_gaps off
to produce:
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
consensus/100% hp..p.lG.GtFG.V..u.h....-.LPKGSMNsc....VAlKphp.t...pE...ph.cEh.hM.plpp.plsphhuls
consensus/90% hp..p.lG.GtFG.V..u.h....-.LPKGSMNsc....VAlKphp.t...pE...ph.cEh.hM.plpp.plsphhuls
consensus/80% lphsKplGsGtFGhVhhGhhhs..-.LPKGSMNsc.hh.VAlKpl+.ts.spE..p-hhcEAtlMtplpH.plVpLhGls
consensus/70% lphsKplGsGtFGhVhhGhhhshs-.LPKGSMNsc.hh.VAlKpl+.ts.spEs.p-hhcEAtlMtplpH.plVpLhGls
Make consensus span low coverage regions, switch off conserved residues
The strict consensus calculation can be relaxed to ignore gaps, so that the consensus is also computed across lower coverage regions. In addition, conserved residue names can be replaced with their consensus classes:
mview ... -consensus on -con_coloring any -con_gaps off -con_ignore singleton
to produce:
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
consensus/100% hp..p.lu.utau.l..u.h....-.ls+uohssc....lul+php.t...p-...ph.c-h.hh.plpp.plsphhuls
consensus/90% hp..p.lu.utau.l..u.h....-.ls+uohssc....lul+php.t...p-...ph.c-h.hh.plpp.plsphhuls
consensus/80% lphs+plusutauhlhhuhhhs..-.ls+uohssc.hh.lul+pl+.ts.sp-..p-hhc-utlhtplp+.pllplhuls
consensus/70% lphs+plusutauhlhhuhhhshs-.ls+uohssc.hh.lul+pl+.ts.sp-s.p-hhc-utlhtplp+.pllplhuls
Switch off consensus classes, show only conserved residues
The consensus classes can be switched off, to leave only conserved residues:
mview ... -consensus on -con_coloring any -con_ignore class
to produce:
cov pid 1 [ . . . . : . . ] 80
1 EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
consensus/100% .......G.G.FG.V........................VA.K.................E...M...............
consensus/90% .......G.G.FG.V........................VA.K.................E...M...............
consensus/80% ....K..G.G.FG.V..G.....................VA.K.................EA..M....H...V.L.G..
consensus/70% ....K..G.G.FG.V..G.....................VA.K.................EA..M....H...V.L.G..
Colours¶
Colourmaps¶
There are default colourmaps for protein and nucleotide (either DNA or RNA)
alignments and consensus lines. MView starts up with the default protein
colourmap selected, as if you had specified a molecule type with -moltype
aa (for “amino acid”).
Alignments
Colourmaps have names, e.g., the default protein alignment colourmap is called
P1 and the default nucleotide colourmap is D1. Alternative alignment
colouring colourmaps are explicitly selected using the -colormap
option. For example, another built-in colouring scheme can be specified with
-colormap CLUSTAL.
Here is the default colormap for proteins:
[P1] #Protein: highlight amino acid physicochemical properties #symbols => color #comment . -> dark-gray #wildcard/mismatch Aa => bright-green #hydrophobic Bb => dark-gray #D or N Cc => yellow #cysteine Dd => bright-blue #negative charge Ee => bright-blue #negative charge Ff => dark-green #large hydrophobic Gg => bright-green #hydrophobic Hh => dark-green #large hydrophobic Ii => bright-green #hydrophobic Kk => bright-red #positive charge Ll => bright-green #hydrophobic Mm => bright-green #hydrophobic Nn => purple #polar Pp => bright-green #hydrophobic Qq => purple #polar Rr => bright-red #positive charge Ss => dull-blue #small alcohol Tt => dull-blue #small alcohol Vv => bright-green #hydrophobic Ww => dark-green #large hydrophobic Yy => dark-green #large hydrophobic Zz => dark-gray #E or Q Xx -> dark-gray #unknown ? -> light-gray #unknown * -> black #stop
The default alignment colormap for nucleotide sequences can be selected using
the -moltype na (or dna or rna) option:
mview ... -moltype na
or by specifying:
mview ... -colormap D1
and is defined as:
[D1] #DNA: highlight nucleotide types #symbols => color #comment . -> dark-gray #wildcard/mismatch Aa => bright-blue #adenosine Cc => dull-blue #cytosine Gg => bright-blue #guanine Tt => dull-blue #thymine Uu => dull-blue #uracil Mm => dark-gray #amino: A or C Rr => dark-gray #purine: A or G Ww => dark-gray #weak: A or T Ss => dark-gray #strong: C or G Yy => dark-gray #pyrimidine: C or T Kk => dark-gray #keto: G or T Vv => dark-gray #not T: A or C or G Hh => dark-gray #not G: A or C or T Dd => dark-gray #not C: A or G or T Bb => dark-gray #not A: C or G or T Nn => dark-gray #any: A or C or G or T Xx -> dark-gray #any ? -> light-gray #unknown
Consensus lines
In addition, the consensus lines optionally displayed below an alignment can
be coloured, and they have their own consensus colourmaps; the default for
proteins is PC1 and for nucleotides it is DC1. Alternative consensus
colouring colourmaps are explicitly selected using the -con_colormap option.
Here is the default consensus colormap for proteins:
[PC1] #Protein consensus: highlight equivalence class #symbols => color #comment . -> dark-gray #unconserved + -> bright-red #positive charge - -> bright-blue #negative charge a -> dark-green #aromatic c -> purple #charged h -> bright-green #hydrophobic l -> bright-green #aliphatic o -> dull-blue #alcohol p -> dull-blue #polar s -> bright-green #small t -> bright-green #turnlike u -> bright-green #tiny
The default consensus colormap for nucleotide sequences can be selected using
the -moltype na (or dna or rna) option:
mview ... -moltype na
or by specifying:
mview ... -con_colormap DC1
and is defined as:
[DC1] #DNA consensus: highlight ring type #symbols => color #comment . -> dark-gray #unconserved r -> purple #purine y -> orange #pyrimidine
Creating new colourmaps¶
The built-in colour palette and colourmaps built from it can be listed from
the command line with -listcolors, and new colour schemes can be loaded
from a file using the -colorfile option.
Predefined colours are defined as in the following short segment of the built
in colour palette obtained with -listcolors -html head to wrap the output
in HTML and display the actual colours:
#color : #RGB color black : #000000 color white : #ffffff color red : #ff0000 color green : #00ff00 color blue : #0000ff color cyan : #00ffff color magenta : #ff00ff color yellow : #ffff00 ...
Here’s an example of a short protein colouring scheme using the built-in colourmap, which is used to explain the syntax:
[CYS] #Protein: highlight cysteines #symbols => color #comment . -> dark-gray #wildcard/mismatch Cc => yellow #cysteine Xx -> dark-gray #unknown ? -> light-gray #unknown
When writing a new protein/nucleotide colouring scheme, scheme names
introduced in square brackets ([CYS], above) are case-insensitive.
Any line or part of a line beginning with a # character is a comment.
Colourings are defined one per line by symbol(s) at the left, an arrow, then
the colour name or RGB code, followed by an optional comment. The symbols at
the left are case-sensitive, and can be given as single characters X or as
a character pair like Xx, where we want both upper- and lowercase to have
the same colour. The special wildcard . symbol sets the base colour to be
used for all symbols in the alignment. Other lines define specific colourings
for sequence symbols of interest. The ordering of lines is not important.
In the example, C or c will be painted yellow; an explicit X or
x residue will be dark grey; an explicit unknown residue ? will be
light gray; any other residue will match the . wildcard and be painted
dark grey.
A symbol to name mapping can use a predefined colour name (as above) or an explicit hexadecimal RGB code like those in the colour palette.
The arrow separating the symbol(s) from the colour code can be double =>
or single -> arrows selecting background or foreground colouring:
If style sheets are not being used, the choice of arrow is unimportant: the supplied colour is used for the foreground, i.e., the output symbol.
If style sheets are in use with
-css on, then=>means that the colour should be applied to the background of the symbol, while->means it should be aplied to the foreground, i.e., the symbol itself.
So, in the CYS example, the symbols *, ?, X, x will be
coloured in the foreground (i.e., the symbols themselves), and C or c
will be displayed as coloured symbols unless -css on is set, in which case
they will appear as coloured bocks.
Coverage and identity¶
MView calculates percent coverage and percent identity of every sequence with respect to a reference sequence, by default the query sequence of a search, or the first row of a sequence alignment.
You can change the reference sequence against which identities are calculated
using the -reference option, which requires either a row number or a
sequence identifier (see Changing the reference sequence).
In addition, you can resort the alignment using the -sort option (see
Sorting by percent coverage or percent identity).
The coverage and identity calculations are defined below.
Percent coverage¶
Percent coverages reported in each alignment row are calculated with respect to the reference sequence (by default, the query or first row):
Percent identity¶
Percent identities reported in each alignment row are calculated with respect to the aligned portion of the reference sequence (usually the query or first row):
Two other calculation possibilities are available: -pcid reference
normalises by the ungapped length of the query or reference sequence, and
-pcid hit normalises by the ungapped length of the hit sequence.
Note: in the case of BLAST MView output, minor deviations from the percentages
reported by BLAST are due to (1) different rounding, and (2) the way MView
assembles a single pseudo-sequence (see Why are some sequence symbols lowercased?) for a hit
composed of multiple HSPs, giving an averaged percent identity. This default
behaviour above is also obtained using the option -pcid aligned.
Data formats¶
Input formats¶
MView supports a variety of input formats covering common sequence database seach and multiple alignment formats. Alternatively, if you can convert some strange alignment to one of the simpler input formats (FASTA, PIR, MSF, plain) you can then read it into MView. See input_formats.
Output formats¶
The default output is plain text showing the alignment together with some header information. HTML markup will be added if any of the HTML-specific or colouring options are set.
However, a number of alternative output formats allow format conversions (e.g., convert a BLAST search to FASTA sequence format) for subsequent processing. See output_formats.
Linking identifiers to external resources¶
Using the -srs on option with HTML output, it is possible to convert
sequence identifiers into links to a sequence database:
mview -in fasta -html head -css on -coloring id -colormap clustal -srs on data.dat
Colored by: identity
cov pid 1 [ . . . . : . . ] 80
1 sp|P00533.2|EGFR_HUMAN 100.0% 100.0% FKKIKVLGSGAFGTVYKGLWIPEGEK---------VKIPVAIKELREATSPK-ANKEILDEAYVMASVDNPHVCRLLGIC
2 sp|Q9I7F7.3|PR2_DROME 97.1% 35.7% ISVNKQLGTGEFGIVQQGVWSNGNE-----------RIQVAIKCLCRERMQS-NPMEFLKEAAIMHSIEHENIVRLYGVV
3 sp|Q08881.1|ITK_HUMAN 90.0% 32.9% LTFVQEIGSGQFGLVHLGYWLN--------------KDKVAIKTIREGAMS---EEDFIEEAEVMMKLSHPKLVQLYGVC
4 sp|Q13308.2|PTK7_HUMAN 97.1% 21.2% IREVKQIGVGQFGAVVLAEMTGLS-XLPKGSMNADGVALVAVKKLKPDVSD-EVLQSFDKEIKFMSQLQHDSIVQLLAIC
5 sp|P34265.4|KIN31_CAEEL 100.0% 31.5% VELTKKLGEGAFGEVWKGKLLKILDA-------NHQPVLVAVKTAKLESMTKEQIKEIMREARLMRNLDHINVVKFFGVA
The identfiers need to conform to patterns such as:
database|accession|identifier
database:identifier
like those produced by the NCBI, EBI or other blast services.
Links will be constructed if the patterns are listed in the SRS.pm
library, which is part of this software. You can modify and extend this file
to include more patterns if you know some Perl and the format of the URLs
needed to access the sequence databases of interest.
Of course, this linking mechanism works for any recognised input data format, not just blast results.
Memory usage and speed¶
Use of memory by MView can be very great, particularly if you try to process complete sets of PSI-BLAST cycles each containing 1000s of hits all at once. Use of most filtering options should reduce memory requirements by cutting down the number of internal data structures created.
In particular, if you only want to see the scoring information and don’t care
about the sequence alignments, you can switch these off with the -sequences
off option, which will also speed up the program.
Likewise, processing each alignment (for example, plus strands and then minus
strands) separately will save memory, or you can use the option -register
off to cause each alignment to be output when ready (by default all
alignments are saved until the end so they can be printed with fields in
vertical register).
Comment row colouring¶
Individual rows can be coloured following a particular scheme by embedding the name of a colourmap in the sequence identifier of a comment line (see above). The sequence identifier must begin with a
#character followed by the name of a colourmap and a colon separator before the identifier string. For example,#MAPor#MAP:commentwould cause the MAP colourmap to be used if it exists. Otherwise, the row will be displayed uncoloured.One use of this might be to colour rows of protein secondary structure assignments. Here is a fragment of an HSSP multiple sequence alignment, which also shows a DSSP-derived secondary structure assignment under the dummy identifier
#DSSP:cov pid 1 [ . . . . : . . . 80 1 0:9wga 100.0% 100.0% XRCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCPNNHCCSQYGHCGFGAEYCGAGCQG 2 2:uniprot|P02876|agi2_whe 99.4% 100.0% -RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCPNNHCCSQYGHCGFGAEYCGAGCQG 3 4:uniprot|P10968|agi1_whe 98.8% 97.6% -RCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQG DSSP ---BGGGTTB--GGG-EE-TTS-EE-SHHHHSTT--SSS-SS--B-GGGGTT---GGG-EE-TTSBEE-SHHHHSTT--BNote 1: MView strips the
#character from the row identifier in the display, but leaves the name of the colourmap. The intention is that the user can define various specialized colourmaps with informative names, as here with DSSP.Note 2: Any number of these rows is allowed, using the same or different colourmaps, and they can be placed anywhere in the alignment.