The code has been tested for the following formats and versions for protein and nucleotide sequences:
Sequence database search programs. See BLAST HSP processing rules for details of BLAST processing by MView.
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+ ok blastn 2.2.25+, 2.2.28+, 2.2.31+ ok blastx 2.2.28+, 2.2.31+ ok tblastn 2.2.28+, 2.2.31+ ok tblastx 2.2.28+, 2.2.31+ ok psiblast 2.2.28+, 2.2.31+ ok
MView option: -in blast (with -outfmt 7 tabular BLAST format)
Program Tested Status blastp 2.2.28+ ok blastn 2.2.28+ ok blastx 2.2.28+ ok tblastn 2.2.28+ ok tblastx 2.2.28+ ok psiblast 2.2.28+ ok
The -outfmt 7 fields or columns recognised by MView are:
Suitable strings of field specifiers 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.
Note: At time of writing, another issue arises with BLAST 2.2.31+, which does not recognise the additional -outfmt 7 field specifiers at all, despite their being documented.
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
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
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
Sequence database search programs.
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
Sequence database search programs:
MView option: -in uvfasta
Program Tested Status fasta 36.07, 36.3.3, 36.3.6, 36.3.7b ok fastx 36.3.3, 36.3.6, 36.3.7b ok fasty 36.3.6, 36.3.7b ok tfastx 36.3.3, 36.3.6, 36.3.7b ok tfasty 36.3.3, 36.3.6, 36.3.7b ok ssearch 36.3.3, 36.3.6, 36.3.7b ok ggsearch 36.3.3, 36.3.6, 36.3.7b ok glsearch 36.3.3, 36.3.6, 36.3.7b ok fastm 35.3.5a, 36.3.6, 36.3.7b experimental fasts 36.3.6, 36.3.7b experimental fastf 36.3.6, 36.3.7b experimental tfastm 36.3.7b experimental tfasts 36.3.7b experimental tfastf 36.3.7b experimental
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
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
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
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
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 '*'.
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.
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