[Bioperl-l] About bioperl issue: get string
Hsueh
lovebaby39 at gmail.com
Wed Dec 23 10:48:55 UTC 2009
Dear all
I use "$hit_u->name" to get "gnl|uv|Z46234.1:664-3444", but I don't know how
to get "P.pastoris DNA for pPIC9K expression vector".
while (my $result_u = $blast_report_u-> next_result ) {
while (my $hit_u = $result_u->next_hit()){
while (my $hsp_u = $hit_u->next_hsp()){
$hit_u->name;
$hsp_u->evalue;
$hsp_u->score;
}
}
}
I will appreciate if you could tell me how to do it.
P.S. How can I download the BioPerl's Manual? (BioPerl's Manual download
link?)
The flow is BLAST result:
-------------------------------------------------------------------------------------------------------------------------------------
BLASTN 2.2.16 [Mar-25-2007]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query=
(458 letters)
Database: UniVec (build 4.0)
2416 sequences; 597,480 total letters
Searching..................................................done
Score E
Sequences producing significant alignments:
(bits) Value
gnl|uv|Z46234.1:664-3444 P.pastoris DNA for pPIC9K expression ve...
26 3.1
gnl|uv|U89673.1:863-1946 Cloning vector pIRES1neo
26 3.1
gnl|uv|U13843.1:1887-9923 pBPV cloning vector
26 3.1
>gnl|uv|Z46234.1:664-3444 P.pastoris DNA for pPIC9K expression vector
Length = 2781
Score = 26.3 bits (13), Expect = 3.1
Identities = 13/13 (100%)
Strand = Plus / Plus
Query: 352 tactaccgccatt 364
|||||||||||||
Sbjct: 2209 tactaccgccatt 2221
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Reginald Hsueh
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