[Bioperl-l] About bioperl issue: get string
Hotz, Hans-Rudolf
hrh at fmi.ch
Wed Dec 23 15:14:06 UTC 2009
Hi
Assuming you are using "SearchIO", try:
$hit_u->description
for more details see: http://www.bioperl.org/wiki/HOWTO:SearchIO
Regards, Hans
On 12/23/09 11:48 AM, "Hsueh" <lovebaby39 at gmail.com> wrote:
> Dear all
>
> I use "$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
> ------------------------------------------------------------------------------
> -------------------------------------------------------
>
> Reginald Hsueh
>
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