Modules

These sections give a small overview about the different functions available in BioSeqDataLib. To have a more detailed look use doxygen to generate the documentation provided for each unit within the source code.

Domain

The domain module allows to read and process domain annotations of proteomes. Although we currently focus more on the Pfam database as source for domain annotations we do try to support other databases as well. Currently we are able to read the following formats:

  • Pfam format (as produced by pfam_scan.pl)
  • domtblout format from hmmscan HMMER
  • ass format as produced by the SUPERFAMILY
  • xdom format

Sequence

This module allows to read sequences in quite a range of different formats including most of the standard formats. It allows as well several basic modification options.

Phylogeny

Domain arrangements as well as sequences change over time. This module helps analyzing these changes by providing basic classes and functions to read and traverse a phylogenetic tree. Additionally it provides some parsimony functions to analyze changes along the tree.

External_interfaces

The purpose of this module is to be able to call different programs with standard parameters. Currently it allows to call different alignment programs, programs needed to construct a tree and annotate a sequence with domains.