Parsing BLAST output

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Parsing BLAST output
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Output of a local BLAST search
less program
Full path to the BLAST output file
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BLAST program used for the search
Reference
Information of the query sequence
Information of the database
One-line summary of the search results
Detailed information for the first 2 hsps of the
first hit Accession number, description,
organism, score, E value, identities, positives,
and alignment
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Sample BLAST output (continued)
Hsp information from the first hit
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Press q to quit the less viewing mode
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• The size of the BLAST output is limited only by
  the free disk space you have in your computer.
  Its virtually impossible to open a large text
  file. Let alone going through the file line by
  line.
• The purpose of parsing BLAST output is to
  extract user-defined information from the BLAST
  output file for clear visualization and
  summarization.

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Search result parsing

• The BioSearchIO system was designed for
  parsing sequence database searches (BLAST, sim4,
  waba, FASTA, HMMER, exonerate, etc.)

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One-line summary of the search results
Load BioSearchIO module
Usage information It will appear if the program
is invoked without arguments
Define the class
Print out the header information
Process each result
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Process each hit
Process each HSP
Control for the number of hits to be extracted
Indicator showing the work is done
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Change directory (cd) to where the perl script
and the BLAST output file are stored
Confirm that the perl script and the BLAST output
are in place
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Oops an error message Its due to Windows and
Unix compatibility.
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Find the file in Windows system and open it with
Notepad
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Select convert to UNIX format in the Format
drop-down menu
After the conversion, save the file and exit
Notepad
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Another error message This is because the perl
interpreter has been installed in another
location (/usr/bin/) while the script is looking
for the perl interpreter in /usr/local/bin
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Now its working !
Solution Create a symbolic link of /usr/bin/perl
in /usr/local/bin Command lnltspacegt-sltspacegt/us
r/bin/perlltspacegt/usr/local/bin/perl
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This is the file youve just generated.
Congratulation! Youve just parsed a BLAST output!
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Lets see how the file looks like, using less.
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Here is how it looks like.
The parsed output is tab-delimited and can be
imported into Excel for better visualization.
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Locate the file in Windows system
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Header row
Query sequence
Accession numbers of the top 3 hits
E values of the top 3 hits
Descriptions of the top 3 hits
Information of each HSP of the top 3 hits