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BLAST Output Formats

Hannes Hauswedell edited this page May 31, 2018 · 7 revisions

Currently three of the native BLAST output formats are supported:

Description legacy BLAST BLAST+ lambda extension
pairwise -m 0 -outfmt 0 .m0
tabular -m 8 -outfmt 6 .m8
tabular with comment lines -m 9 -outfmt 7 .m9

Custom columns

For the tabular and tabular with comments lines formats you may specify the order and column composition. The columns have the same specifiers as in BLAST+, right now all of the above are supported via the command line option --output-columns. Please note that it is recommend to keep the first 12 columns as they are for compatibility, i.e. first write std and then custom columns that you want, e.g.--output-columns "std score qframe".

specifier description since
std Default 12 columns (Query Seq-id, Subject Seq-id, Percentage of identical matches, Alignment length, Number of mismatches, Number of gap openings, Start of alignment in query, End of alignment in query, Start of alignment in subject, End of alignment in subject, Expect value, Bit score)
qseqid Query Seq-id
qlen Query sequence length
sseqid Subject Seq-id
slen Subject sequence length
qstart Start of alignment in query
qend End of alignment in query
sstart Start of alignment in subject
send End of alignment in subject
evalue Expect value
bitscore Bit score
score Raw score
length Alignment length
pident Percentage of identical matches
nident Number of identical matches
mismatch Number of mismatches
positive Number of positive-scoring matches
gapopen Number of gap openings
gaps Total number of gaps
ppos Percentage of positive-scoring matches
frames Query and subject frames separated by a '/'
qframe Query frame
sframe Subject frame
staxids Subject taxonomy ID(s) seperated by ; (Taxonomic Workflows) 1.9.2
lcaid¹ Lowest common ancestor name (Taxonomic Workflows) 1.9.2
lcataxid¹ Lowest common ancestor taxonomy ID (Taxonomic Workflows) 1.9.2

¹ Not part of NCBI Blast.