When I do local BLAST with the parameter -m 8, I find that one query sequence can match the same subject sequence at several parts. I wonder if there is some tool that can read the BLAST m8 output and graphically display the matched regions, just as the online NCBI BLAST does. If there is such a tool, it will be much easier to view the results.
3 answers
(not tested) I would transform the data using a BLAST2GFF (for example, this one found via google: http://jperl.googlecode.com/svn-history/r16/trunk/Blast2Gff.pl) and display the resulting GFF track (see this previous question: What Tools/Libraries Do You Use To Visualize Genomic Feature Data? )
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written
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Pierre Lindenbaum
I installed wwwblast locally, essentially created a local version of blast server. It's working quite good if you have a linux distro or mac os x with apache pre-installed. Or you can do blast2gff like Pierre suggested but displaying gffs is more involved. Another option is here: http://www.bioperl.org/wiki/HOWTO:Graphics. I had a lot fun using this and I think this is very very powerful, it's essentially the based of Gbrowse.
For those who are still interested, heare are the script: http://etutorials.org/Misc/blast/Part+VI+Appendixes/Appendix+D.+blast-imager.pl/
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