[Bioperl-l] About bioperl issue: get string

[Hotz, Hans-Rudolf]

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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