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 Tested Status
blastp 2.2.25+, 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok
blastn 2.2.25+, 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok
blastx 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok
tblastn 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok
tblastx 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok
psiblast 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok

MView option: -in blast (with -outfmt 7 tabular BLAST format)

Program Tested Status
blastp 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok
blastn 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok
blastx 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok
tblastn 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok
tblastx 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok
psiblast 2.2.28+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.6.0+ ok

The -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, 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’

MView will silently ignore any fields other than those listed above. The field ordering given does not matter as MView identifies this automatically.

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 Tested Status
blastp 2.2.5, 2.2.6 ok
blastn 2.2.6 ok
blastx 2.2.6 ok
tblastn 2.2.6 ok
tblastx 2.2.6 ok
psiblast 2.2.6 ok
phiblast 2.2.6 ok

BLAST series 2.0

MView option: -in blast

Program Tested Status
blastp 2.0.4, 2.0.5, 2.0.9, 2.0.10 ok
blastn 2.0.4, 2.0.5, 2.0.9, 2.0.14 ok
blastx 2.0.5, 2.0.9 ok
tblastn 2.0.5, 2.0.10 ok
tblastx 2.0.5 ok
psiblast 2.0.2, 2.0.4, 2.0.5, 2.0.6, 2.0.10 ok
phiblast 2.0.9 ok

BLAST series 1.4

MView option: -in blast

Program Tested Status
blastp 1.4.7, 1.4.9 ok
blastn 1.4.9 ok
blastx 1.4.9 ok
tblastn 1.4.9 ok
tblastx 1.4.9 ok

WashU-BLAST family

Sequence database search programs.

WU-BLAST series 2.0

MView option: -in blast

Program Tested Status
blastp 2.0a13, 2.0a19, 2.0 ok
blastn 2.0a19, 2.0 ok
blastx 2.0a19, 2.0 ok
tblastn 2.0a19, 2.0 ok
tblastx 2.0a19, 2.0 ok

Uni. Virginia FASTA family

Sequence database search programs:

FASTA series 36

MView option: -in uvfasta

Program Tested Status
fasta 36.07, 36.3.3, 36.3.6, 36.3.7b, 36.3.8e ok
fastx 36.3.3, 36.3.6, 36.3.7b, 36.3.8e ok
fasty 36.3.6, 36.3.7b, 36.3.8e ok
tfastx 36.3.3, 36.3.6, 36.3.7b, 36.3.8e ok
tfasty 36.3.3, 36.3.6, 36.3.7b, 36.3.8e ok
ssearch 36.3.3, 36.3.6, 36.3.7b, 36.3.8e ok
ggsearch 36.3.3, 36.3.6, 36.3.7b, 36.3.8e ok
glsearch 36.3.3, 36.3.6, 36.3.7b, 36.3.8e ok
fastm 35.3.5a, 36.3.6, 36.3.7b, 36.3.8e experimental
fasts 36.3.6, 36.3.7b, 36.3.8e experimental
fastf 36.3.6, 36.3.7b, 36.3.8e experimental
tfastm 36.3.7b, 36.3.8e experimental
tfasts 36.3.7b, 36.3.8e experimental
tfastf 36.3.7b, 36.3.8e experimental

FASTA series 35

MView option: -in uvfasta

Program Tested Status
fasta 35.04 ok
tfastx 35.04 ok
ssearch 35.04 ok
ggsearch 35.04 ok
glsearch 35.04 ok

FASTA series 34

MView option: -in uvfasta

Program Tested Status
fasta34 34.26.5 ok

FASTA series 3.0 - 3.4

MView option: -in uvfasta

Program Tested Status
fasta 3.0t76, 3.1t07, 3.2t01, 3.2t05, 3.2t07  
3.2t05, 3.2t07, 3.3t01, 3.3t07, 3.4t23 ok
fastx 3.4t23 ok
fasty 3.4t23 ok
tfasta 3.4t23 ok
tfastx 3.0t82, 3.4t23 ok
tfasty 3.4t23 ok
tfastxy 3.1t07 ok

FASTA series 2

MView option: -in uvfasta

Program Tested Status
fasta 2.0u ok
tfastx 2.0u63 ok

FASTA series 1

MView option: -in uvfasta

Program Tested Status
fasta 1.6c24 ok

CLUSTAL/aln

The CLUSTAL family of multiple sequence alignment programs produce ‘aln’ format.

MView option: -in clustal

Program Tested Status
CLUSTAL 1.60, 1.70, 1.83, 2.1 ok

HSSP

The HSSP multiple sequence alignment format is produced by the MaxHom protein sequence and structure homology alignment program.

MView option: -in hssp

Program Tested Status
HSSP 1.0 1991 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