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+

blastp

ok

ok

ok

ok

ok

ok

ok

ok

ok

blastn

ok

ok

ok

ok

ok

ok

ok

ok

ok

blastx

.

ok

ok

ok

ok

ok

ok

ok

ok

tblastn

.

ok

ok

ok

ok

ok

ok

ok

ok

tblastx

.

ok

ok

ok

ok

ok

ok

ok

ok

psiblast

.

ok

ok

ok

ok

ok

ok

ok

ok

phiblast

.

.

.

.

.

.

.

.

.

Program

2.9.0+

2.10.0+

2.10.1+

2.16.0+

blastp

ok

ok

ok

ok

blastn

ok

ok

ok

ok

blastx

ok

ok

ok

ok

tblastn

ok

ok

ok

ok

tblastx

ok

ok

ok

ok

psiblast

ok

ok

ok

ok

phiblast

ok

ok

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+

blastp

ok

ok

ok

ok

ok

ok

ok

ok

ok

blastn

ok

ok

ok

ok

ok

ok

ok

ok

ok

blastx

ok

ok

ok

ok

ok

ok

ok

ok

ok

tblastn

ok

ok

ok

ok

ok

ok

ok

ok

ok

tblastx

ok

ok

ok

ok

ok

ok

ok

ok

ok

psiblast

ok

ok

ok

ok

ok

ok

ok

ok

ok

phiblast

.

.

.

.

.

.

.

.

ok

Program

2.10.0+

2.10.1+

2.16.0+

blastp

ok

ok

ok

blastn

ok

ok

ok

blastx

ok

ok

ok

tblastn

ok

ok

ok

tblastx

ok

ok

ok

psiblast

ok

ok

ok

phiblast

ok

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 34

MView option: -in uvfasta

Program

34.26.5

fasta34

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

fasta

ok

.

ok

ok

ok

ok

ok

ok

ok

fastx

.

.

.

.

.

.

.

.

.

fasty

.

.

.

.

.

.

.

.

.

tfasta

.

.

.

.

.

.

.

.

.

tfastx

.

ok

.

.

.

.

.

.

.

tfasty

.

.

.

.

.

.

.

.

.

tfastxy

.

.

ok

.

.

.

.

.

.

Program

3.3t07

3.4t23

fasta

ok

ok

fastx

.

ok

fasty

.

ok

tfasta

.

ok

tfastx

.

ok

tfasty

.

ok

tfastxy

.

.

FASTA series 2

MView option: -in uvfasta

Program

2.0u

2.0u63

fasta

ok

.

tfastx

.

ok

FASTA series 1

MView option: -in uvfasta

Program

1.6c24

fasta

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'.

FASTA

The classic FASTA (or Pearson) sequence file format.

MView option: -in fasta

MSF

The Wisconsin Package GCG Multiple Sequence File format.

MView option: -in msf

PIR

The Protein Information Resource sequence file format.

MView option: -in pir

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