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+ 2.8.0+
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
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

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+ 2.8.0+
blastp ok ok ok ok ok ok ok ok
blastn 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

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
blastp ok ok
blastn . ok
blastx . ok
tblastn . ok
tblastx . ok
psiblast . ok
phiblast . 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
fasta ok ok . ok ok ok ok ok
fastx . ok . ok ok ok ok ok
fasty . . . ok ok ok ok ok
tfastx . ok . ok ok ok ok ok
tfasty . ok . ok ok ok ok ok
ssearch . ok . ok ok ok ok ok
ggsearch . ok . ok ok ok ok ok
glsearch . ok . ok ok ok ok ok
fastm . . expt expt expt expt expt expt
fasts . . . expt expt expt expt expt
fastf . . . expt expt expt expt expt
tfastm . . . . expt expt expt expt
tfasts . . . . expt expt expt expt
tfastf . . . . 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 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 . . . . . . . .

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, only the first one will be output. You can extract a particular block, say the second one, with -block 2, or all blocks with -block '*'.

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