Hello all,
I'm an avid user of mpiblast 1.4.0, and it has been working phenomenally
for me. Thanks to the development team for the great work! I hope this
isn't a little too off topic, since I don't particularly have a problem
with mpiblast now, but hope someone can help. After many searches on
Google and asking around I couldn't find the answer. I'm sure someone
here on this list knows BLAST better than I do:
Blast Output files usually have something like this on each hit:
...
>gb|AE000111.1|AE000111 Escherichia coli K-12 MG1655 section 1 of 400 of
the complete genome
Length = 10596
Score = 2.044e+04 bits (10312), Expect = 0.0
Identities = 10344/10360 (99%)
Strand = Plus / Plus
...
This database that I was querying against was Ecoli, so there's already
a bunch of description info for each. The ">gb|AE000111.1|AE000111" is
a hyperlink that takes me to where I can get more info like the actual
sequence associated with it.
However, when I query against my own Blast database these links would of
course not be there. Is there a way where I can format my personal
blast databases to include links just like the well annotated ones?
I thought of using a script to parse and add links onto the Blast output
file. However, I have my own customized system where using a script do
a post-parse search & replace would not solve all my problems. I really
do prefer preformatting a database somehow with my info. I have no idea
where to start, and this forum post I found gave me a little insight:
http://www.bio.net/bionet/mm/bio-www/2002-January/001056.html
It mentions the fastacmd utility as well as making my own "gi"'s ? I'm
not exactly sure what any of this meant, nor have I ever used fastacmd.
Thanks in advance for your time and sorry if this isn't exactly an
mpiblast question except kind of just for one-- mpiformatdb shouldn't
have a problem formatting personal databases the way I want with all the
links and stuff right?
Regards,
Ray C.
Univ. of California, Davis
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