WU BLAST 2.0 Tabular Output

Tabular Output Description

Tab-delimited output is available from WU-BLAST 2.0 when mformat=2 or mformat=3 are specified on the command line. The latter option causes comment lines beginning with a pound sign (#) to be reported in the output, as well. If a query sequence identifier begins with a pound sign (#) or a backslash (\), it is escaped with a backslash; subject sequence identifiers are always reported “as is”.

The standard tokens reported in tabular output are shown in the Table 1 below. Table 2 describes tokens that appear only if certain other command line options are specified.

This file is available in PDF format here.

Table 1. Constitutively Expressed Entities in Tabular Output

#	Label	Description
1	`qid`	query sequence identifier
2	`sid`	subject (database) sequence identifier
3	`E`	the expectation or E-value
4	`N`	the number of scores considered jointly in computing E
5	`Sprime`	the normalized alignment score, expressed in units of bits
6	`S`	the raw alignment score
7	`alignlen`	the overall length of the alignment including any gaps
8	`nident`	the number of identical letter pairs
9	`npos`	the number of letter pairs contributing a positive score
10	`nmism`	the number of mismatched letter pairs
11	`pcident`	percent identity over the alignment length (as a fraction of `alignlen`)
12	`pcpos`	percent positive letter pairs over the alignment length (as a fraction of `alignlen`)
13	`qgaps`	number of gaps in the query sequence
14	`qgaplen`	total length of all gaps in the query sequence
15	`sgaps`	number of gaps in the subject sequence
16	`sgaplen`	total length of all gaps in the subject sequence
17	`qframe`	the reading frame in the query sequence (`+0` for protein sequences in `BLASTP` and `TBLASTN` searches)
18	`qstart`	the starting coordinate of the alignment in the query sequence
19	`qend`	the ending coordinate of the alignment in the query sequence
20	`sframe`	the reading frame in the subject sequence (`+0` for protein sequences in `BLASTP` and `BLASTX` searches)
21	`sstart`	the starting coordinate of the alignment in the subject sequence
22	`send`	the ending coordinate of the alignment in the subject sequence

Table 2. Conditionally Expressed Entities in Tabular Output

Label	Description	Inducing Parameter(s)
`group`	the “topcombo” group number for a set of HSPs	`topcomboN`, `topcomboE`
`links`	a dash-delimited list of consistent HSP numbers whose scores were used jointly to compute the E-value; the number of the current HSP (the HSP described by the current line of output) is enclosed in parentheses	`links`

Last modified: 2005-03-24

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