AB-BLAST 3.0 Tabular Output

Tabular Output Description

Tab-delimited output is available from AB-BLAST 3.0 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.

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: 2009-01-24

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