Input formats¶
The code has been tested for the following formats and versions for protein and nucleotide sequences:
NCBI BLAST family¶
Sequence database search programs. See BLAST HSP processing rules for details of BLAST processing by MView.
BLAST+¶
Modern BLAST can generate output in a number of formats; run blastp -help to see what is available.
MView can process two of these: the default BLAST output format (also obtained with the BLAST command line option -outfmt 0) and a commented tabular format produced with -outfmt 7. MView support and testing is as follows.
MView option: -in blast
(with the default BLAST format)
Program 2.2.25+ 2.2.28+ 2.2.31+ 2.3.0+ 2.4.0+ 2.5.0+ 2.6.0+ 2.7.1+ 2.8.1+ 2.9.0+ 2.10.0+ blastp ok ok ok ok ok ok ok ok ok ok ok blastn ok ok ok ok ok ok ok ok ok ok ok blastx . ok ok ok ok ok ok ok ok ok ok tblastn . ok ok ok ok ok ok ok ok ok ok tblastx . ok ok ok ok ok ok ok ok ok ok psiblast . ok ok ok ok ok ok ok ok ok ok phiblast . . . . . . . . . ok ok
MView option: -in blast
(with -outfmt 7 tabular BLAST format)
Program 2.2.28+ 2.2.31+ 2.3.0+ 2.4.0+ 2.5.0+ 2.6.0+ 2.7.1+ 2.8.1+ 2.9.0+ 2.10.0+ blastp ok ok ok ok ok ok ok ok ok ok blastn ok ok ok ok ok ok ok ok ok ok blastx ok ok ok ok ok ok ok ok ok ok tblastn ok ok ok ok ok ok ok ok ok ok tblastx ok ok ok ok ok ok ok ok ok ok psiblast ok ok ok ok ok ok ok ok ok ok phiblast . . . . . . . . ok ok
The main -outfmt 7 fields or columns recognised by MView are:
- std to report standard fields: qaccver, saccver, pident, length, mismatch, gapopen, qstart, qend, sstart, send, evalue, bitscore;
- qseq, sseq to report the query and sbjct sequences;
- stitle or salltitles to report the sbjct descriptions;
- qframe to report the query frame;
- sframe to report the sbjct frame.
When running blast with tabular output, minimal field specifiers suitable for input to MView are:
blastp -outfmt ‘7 std qseq sseq stitle’
blastn -outfmt ‘7 std qseq sseq stitle’
blastx -outfmt ‘7 std qseq sseq stitle qframe’
tblastn -outfmt ‘7 std qseq sseq stitle sframe’
tblastx -outfmt ‘7 std qseq sseq stitle qframe sframe’
psiblast -outfmt ‘7 std qseq sseq stitle’
Additional fields that are currently recognised by MView are:
- staxid
- ssciname
- scomname
- sblastname
- sskingdom
- staxids
- sscinames
- scomnames
- sblastnames
- sskingdoms
If present, these are passed through in the format conversions (-out fasta, -out pir, -out rdb) and to the normal MView display mode where they appear as extra columns at the right margin of the alignment. Having very variable field widths they may appear badly aligned vertically. To disable them, use the -label8 option.
MView will silently ignore any fields other than those listed above.
Note: There are some differences in the output (seen in BLAST 2.2.28+) produced by the default BLAST format versus -outfmt 7. The latter lacks the list of ranked database hits and best scores and their associated fragment counts, N. Unfortunately this can obscure interpretation of the results when there are many alternative alignments for a given database hit (see BLAST HSP processing rules) so that in certain cases the MView output will be slightly different; this is most noticeable with tblastx.
Note: A strange behaviour has been seen with psiblast 2.2.28+, where the first database search produces many more hits than subsequent iterations including the final iteration when run using the default output format. Using -outfmt 7 on the exact same search produces more consistent sets of hits.
BLAST series 2.2¶
MView option: -in blast
Program 2.2.5 2.2.6 2.2.9 blastp ok ok ok blastn . ok ok blastx . ok ok tblastn . ok ok tblastx . ok ok psiblast . ok ok phiblast . ok ok
BLAST series 2.0¶
MView option: -in blast
Program 2.0.2 2.0.4 2.0.5 2.0.6 2.0.9 2.0.10 2.0.14 blastp . ok ok . ok ok . blastn . ok ok . ok . ok blastx . . ok . ok . . tblastn . . ok . . ok . tblastx . . ok . . . . psiblast ok ok ok ok . ok . phiblast . . . . ok . .
BLAST series 1.4¶
MView option: -in blast
Program 1.4.7 1.4.9 blastp ok ok blastn . ok blastx . ok tblastn . ok tblastx . ok
WashU-BLAST family¶
Sequence database search programs.
WU-BLAST series 2.0¶
MView option: -in blast
Program 2.0a13 2.0a19 2.0 blastp ok ok ok blastn . ok ok blastx . ok ok tblastn . ok ok tblastx . ok ok
Uni. Virginia FASTA family¶
Sequence database search programs:
FASTA series 36¶
MView option: -in uvfasta
Program 36.07 36.3.3 35.3.5a 36.3.6 36.3.7b 36.3.8e 36.3.8f 36.3.8g 36.3.8h fasta ok ok . ok ok ok ok ok ok fastx . ok . ok ok ok ok ok ok fasty . . . ok ok ok ok ok ok tfastx . ok . ok ok ok ok ok ok tfasty . ok . ok ok ok ok ok ok ssearch . ok . ok ok ok ok ok ok ggsearch . ok . ok ok ok ok ok ok glsearch . ok . ok ok ok ok ok ok fastm . . expt expt expt expt expt expt expt fasts . . . expt expt expt expt expt expt fastf . . . expt expt expt expt expt expt tfastm . . . . expt expt expt expt expt tfasts . . . . expt expt expt expt expt tfastf . . . . expt expt expt expt expt
where ‘expt’ indicates that MView parses and processes the format, but the results may not be particularly useful, hence ‘experimental’.
FASTA series 35¶
MView option: -in uvfasta
Program 35.04 fasta ok tfastx ok ssearch ok ggsearch ok glsearch ok
FASTA series 3.0 - 3.4¶
MView option: -in uvfasta
Program 3.0t76 3.0t82 3.1t07 3.2t01 3.2t05 3.2t07 3.2t05 3.2t07 3.3t01 3.3t07 3.4t23 fasta ok . ok ok ok ok ok ok ok ok ok fastx . . . . . . . . . . ok fasty . . . . . . . . . . ok tfasta . . . . . . . . . . ok tfastx . ok . . . . . . . . ok tfasty . . . . . . . . . . ok tfastxy . . ok . . . . . . . .
CLUSTAL/aln¶
The CLUSTAL family of multiple sequence alignment programs produce ‘aln’ format.
MView option: -in clustal
Version 1.60 1.70 1.83 2.1 CLUSTAL ok ok ok ok
HSSP/Maxhom¶
The HSSP multiple sequence alignment format is produced by the MaxHom protein sequence and structure homology alignment program.
MView option: -in hssp
Version 1.0 1991 HSSP ok
MAF¶
The UCSC Multple Alignment Format.
MView option: -in maf
MAF files contain distinct alignment blocks. By default, all blocks will be
output. You can extract a particular block, say the second one, with -block
2
, or several with -block '1,2,7'
.
plain¶
A simple multiple sequence alignment format.
MView option: -in plain
This is composed of rows of identifier and sequence in two columns like:
identifier1 sequence1 identifier2 sequence2 identifier3 sequence3
and can contain comment lines starting with #
. Identifiers and sequences
must not contain any whitespace as this is used to separate the columns. The
sequences need not be aligned vertically, but they must all be the same
length. Use -
and/or .
characters for gaps.
Unsupported¶
A few other formats were implemented for specific use-cases and are not maintained:
Format MView option Status MIPS-ALN -in mips
experimental MULTAS/MULTAL -in multas
experimental jnet -z -in jnet
experimental