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Output formats

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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.

BLAST+

MView option: -in blast

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

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
psi-blast 2.2.6 ok
phi-blast 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
psi-blast 2.0.2, 2.0.4, 2.0.5, 2.0.6, 2.0.10 ok
phi-blast 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 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

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