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Modules and placement of functions
pappewaio edited this page Sep 30, 2012
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This page will act as an overview page for where all functions are stored within modules.
- 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
- findAltStart.pm
- findParalogs.pm
- multipleAlign.pm
- HashRoutines.pm
- MapRoutines.pm
- findAltStart.pm - findAltStart, findGaps.
- findParalogs.pm - findParalogs, makeTree
- multipleAlign.pm - multipleAlign
- HashRoutines.pm - mkHash, make_gbk_hash, parse_orthomcl_file, parse_groups
- MapRoutines.pm - get_gene, translateToProt