Documentation

  • Bioperl
  • biodesign.pod - Bioperl Design Documentation
  • Bioperl
  • Bioscripts
  • BioPerlTutorial - a tutorial for bioperl
  • generate_histogram.pl - Generate a histogram of Bio::DB::GFF features
  • process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
  • ncbi_2_gff.pl - Massage NCBI chromosome annotation into GFF-format suitable for Bio::DB::GFF
  • process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
  • process_wormbase.pl - Massage WormBase GFF files into a version suitable for the Generic Genome Browser
  • dbfetch - generic CGI program to retrieve biological database entries in various formats and styles (using SRS)
  • feature_draw.pl - Render a Bio::Graphics Feature File
  • bpfetch.pl - fetches sequences from bioperl indexed databases
  • bpindex.pl - indexes files for use by bpfetch
  • longorf - perl script to find the longest ORF of a sequence
  • seq_length.pl - lists the number of bases and number of sequences in specified sequence database files
  • gff2ps - you will want to change this script
  • remote_blast.pl - script for submitting jobs to a remote blast server (ncbi blast queue at this time)
  • tree_from_seqsearch - builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)

Modules

Provides