[Bioperl-l] use Bio::Search::Tiling::MapTiling

Mark A. Jensen maj at fortinbras.us
Tue Nov 16 01:08:25 UTC 2010

Hi Wei, 
You'll need to install the trunk code to access this method; the "release" is woefully out of date (not that I'm helping much on that these days). Use git to obtain the latests bioperl-live and bioperl-run from https://github.com/bioperl/, or the synchronized repos
----- Original Message ----- 
  From: Shao, Wei (NIH/NCI) [C] 
  To: Mark A Jensen 
  Sent: Monday, November 15, 2010 10:47 AM
  Subject: use Bio::Search::Tiling::MapTiling

Dear Dr. Jensen, I am looking for a bioperl module that can be used to concatenate HSP from a blast into a sequence. I found that your Bio::Search::Tiling::MapTilingcan do exactly that. I used your example script to test it. I got an error message:“Can't locate object method "get_tiled_alns" via package "Bio::Search::Tiling::MapTiling" at get_hsp.pl line 29, <GEN1> line 2630”.It seems that method “get_tiled_alns” is not in the bioperl we installed. Is that possible? The script I used is this one:  use Bio::SearchIO;use Bio::Search::Tiling::MapTiling # Note that to get one hit, the user first blasts# the set of contigs against single sequence, the reference sequence.# The result of this BLAST run is in 'contig_tile.bls' $blio = Bio::SearchIO->new( -file => 'contig_tile.bls');$result = $blio->next_result;$hit = $result->next_hit;$tiling = Bio::Search::Tiling::MapTiling->new($hit);@alns = $tiling->get_tiled_alns('query'); # here's the concatenation:$concat_seq_obj = $alns[0]->get_seq_by_id('query'); 

  Best regards,



  Wei Shao, Ph.D. [Contractor] 
  Bioinformatics Analyst IV

  Advanced Biomedical Computing Center/HIV Drug Resistance Program
  SAIC-Frederick, Inc. 

  National Cancer Institute at Frederick
  P.O. Box B, Frederick, MD 21702
  Phone: 301/846-6021

  Fax:  301/846-6013
  Email:  shaow at mail.nih.gov

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