[Bioperl-l] [Bioperl]problem with E-value

lidaof lidaof at gmail.com
Thu Jan 18 00:02:30 EST 2007


Hi Chris,Sendu,

sorry for later reply!

i installed the new NCBI blast 2.2.15(blast-2.2.15-ia32-linux.tar.gz) on a
CentOS server
and the query sequence is the fasta sequence retrieved from NCBI(Soybean's
EST sequence)
because the sequence got from NCBI was not annotated
so i build a plant protein blast database(by formatdb command) using
uniprot's plant protein sequence(plantUniP_withIPR.pep)

the i do the blastx using the EST sequence against protein sequence
the command is "blastall -p blastx -i soybean_est -d plantUniP_withIPR.pep
-a 4 -b 5 -v 5 -o soybean_est_blastx &"

about 6 days later,i got the output result of blastx.
the i wrote a script to extract the best hit's description to annotate each
sequence
that's exactly i do

Cheers
Li


On 1/18/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
> Li, Sendu,
>
> I have committed a fix for this to CVS.  Could you check it to make
> sure everything is kosher?
>
> The fix should work for your (Li's) BLAST report example as well as
> multiquery BLAST reports.
>
> chris
>
> On Jan 17, 2007, at 12:17 PM, Chris Fields wrote:
>
> > Li, Sendu,
> >
> > Following up on this, I generated two new multiquery BLAST reports
> > (BLASTP and BLASTX) from the NCBI BLAST server.  I can't reproduce
> > output similar to Li's example (where the BLASTX header line appears
> > over and over).  It is entirely possible that a local v. 2.2.15 BLAST
> > installation would generate different output.
> >
> > Li, was the example file you sent generated from single query BLAST
> > runs where the output was appended to the same file, or were they
> > generated from a single BLAST run where the queries were all in one
> > file?  There is a significant difference between the two.
> >
> > Regardless, I am able to reproduce a bug where hits aren't created
> > properly from BLAST hit tables (which should be easy to fix).  I'll
> > file a bug report and work on this.
> >
> > As a general note, if you are only interested in hits and not
> > alignments you probably shouldn't use the regular BLAST text output.
> > Try using -m8 -r -m9 BLAST tabular output and 'blasttable' parsing
> > instead of 'blast' and maybe switch event handlers (all in the
> > SearchIO HOWTO).
> >
> > chris
> >
> > On Jan 17, 2007, at 11:03 AM, Chris Fields wrote
> > ...
> >> ...
> >> I plan on generating a new BLAST report (from the web, since I don't
> >> have 2.2.15 installed) with multiple queries and no alignments to see
> >> what happens (i.e. see if the new multiquery report is similar to
> >> this one).  If so, there is a 'wrap-up' section of the parser, where
> >> hit data not in alignments (in the table only) is used to generate
> >> Hit objects; it's dropping this data likely b/c there is no regex
> >> signalling the next result event.
> >>
> >> chris
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


-- 
Li


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