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Biology Articles » Bioinformatics » Introductory Workbook on Perl for Biology Students » 14. Bio-perl programme to retrieve DNA sequence from swissprot

14. Bio-perl programme to retrieve DNA sequence from swissprot
- Introductory Workbook on Perl for Biology Students

This program uses the bioperl package to connect to the internet and get a Swissprot sequence from the internet databases using the get_sequence and is saved in $seq_object. The blast_sequence blasts a sequence against standard databases at NCBI and the result of the blast is stored in $blast_result. The write_blast writes a blast report out to a file. In this case the file name is raol1.blast.

 

  1. #!/usr/bin/perl -w

 

  1. use Bio::Perl;

 

  1. $seq_object = get_sequence('swissprot', "ROA1_HUMAN");
  2. $blast_result = blast_sequence($seq_object);
  3. write_blast(">raol1.blast",$blast_result);
  4. exit;

rating: 3.70 from 114 votes | updated on: 30 Jan 2009 | views: 95785 |

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