# 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+ | 2.9.0+ | 2.10.0+
> --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
> blastp | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> blastn | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> blastx | . | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> tblastn | . | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> tblastx | . | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> psiblast | . | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> phiblast | . | . | . | . | . | . | . | . | . | 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+ | 2.10.0+
> --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
> blastp | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> blastn | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> blastx | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> tblastn | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> tblastx | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> psiblast | ok | ok | ok | ok | ok | ok | ok | ok | ok | ok
> phiblast | . | . | . | . | . | . | . | . | 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 | 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, 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