Reformat BLAST reports with blast_formatter

It may be helpful to view the same BLAST results in different formats. A user may first parse the tabular format looking for matches meeting a certain criteria, then go back and examine the relevant alignments in the full BLAST report. He may also first look at pair-wise alignments, then decide to use a query-anchored view. Viewing a BLAST report in different formats has been possible on the NCBI BLAST web site since 2000, but has not been possible with stand-alone BLAST runs. The blast_formatter allows this, if the original search produced blast archive format using the –outfmt 11 switch. The query sequence, the BLAST options, the masking information, the name of the database, and the alignment are written out as ASN.1 (a structured format similar to XML). The –max_target_seqs option should be used to control the number of matches recorded in the alignment. The blast_formatter reads this information and formats a report. The BLAST database used for the original search must be available, or the sequences need to be fetched from the NCBI, assuming the database contains sequences in the public dataset. The box below illustrates the procedure. A blastn run first produces the BLAST archive format, and the blast_fomatter then reads the file and produces tabular output.

Blast_formatter will format stand-alone searches performed with an earlier version of a database if both the search and formatting databases are prepared so that fetching by sequence ID is possible. To enable fetching by sequence ID use the –parse_seqids flag when running makeblastdb, or (if available) download preformatted BLAST databases from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ using update_blastdb.pl (provided as part of the BLAST+ package). Currently the blast archive format and blast_formatter do not work with database free searches (i.e., -subject rather than –db was used for the original search).

$ echo 1786181 | blastn -db ecoli -outfmt 11 -out out.1786181.asn
$ blast_formatter -archive out.1786181.asn -outfmt "7 qacc sacc evalue
qstart qend sstart send"
# BLASTN 2.2.24+
# Query: gi|1786181|gb|AE000111.1|AE000111 Escherichia coli K-12 MG1655
section 1 of 400 
# Database: ecoli
# Fields: query acc., subject acc., evalue, q. start, q. end, 
s. start, s. end
# 85 hits found
AE000111        AE000111        0.0     1       10596   1       10596
AE000111        AE000174        8e-30   5565    5671    6928    6821
AE000111        AE000394        1e-27   5587    5671    135     219
AE000111        AE000425        6e-26   5587    5671    8552    8468
AE000111        AE000171        3e-24   5587    5671    2214    2130
AE000111        AE000171        1e-23   5587    5670    10559   10642
AE000111        AE000376        1e-22   5587    5675    129     42
AE000111        AE000268        1e-22   5587    5671    6174    6090
AE000111        AE000112        1e-22   10539   10596   1       58
AE000111        AE000447        5e-22   5587    5670    681     598
AE000111        AE000344        6e-21   5587    5671    4112    4196
AE000111        AE000490        2e-20   5584    5671    4921    4835
AE000111        AE000280        2e-20   5587    5670    12930   12847