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Modules and placement of functions

pappewaio edited this page Sep 30, 2012 · 13 revisions

This page will act as an overview page for where all functions are stored within modules.

All Sub Routines:

  • findAltStart Finds alternative start codon. Depends on: getGene, TranslateToProt
  • translateToProt Uses Bioperl to translate DNA sequence to Amino Acid sequence.
  • findGaps Returns the ids of sequences with more than the specified number of gaps.
  • get_gene Returns subsequence from gene. e.g. a gene.
  • mkHash make hash file with id as key and DNA or Amino Acid sequence as value.
  • makeTree returns a bio align.
  • make_gbk_hash returns hash with genbank annotation
  • findParalogs returns an array with all species having 2 or more genes. Depends on: checkIfParalogs, checkIfParalogsComplicated
  • checkIfParalog returns TRUE if a troublesome paralog for the 2 paralog case.
  • checkIfParalogsComplicated returns TRUE if a troublesome paralog for the <2 paralog case.
  • multipleAlign Returns a string that is aligned.
  • parse_orthomcl_file returns a hash for all orhtomcl-group, Depends on: parse_groups
  • parse_groups returns a hash for all orhtomcl-group

Function Specific Modules:

  • findAltStart.pm
  • findParalogs.pm
  • multipleAlign.pm

More General Modules

  • HashRoutines.pm
  • MapRoutines.pm

Modules Contains:

Specific Modules

  • findAltStart.pm - findAltStart, findGaps.
  • findParalogs.pm - findParalogs, makeTree
  • multipleAlign.pm - multipleAlign

General Modules

  • HashRoutines.pm - mkHash, make_gbk_hash, parse_orthomcl_file, parse_groups
  • MapRoutines.pm - get_gene, translateToProt