[Bioperl-l] Bio::SearchIO - Accessing Model parameters (score, evalue, description)
selvik at ufl.edu
Tue Jun 27 08:54:48 EDT 2006
(I am new to Bioinformatics and Bioperl, so please apologize if I
get my terminology wrong)
I am currently using Bio::SearchIO to parse HMMPFAM reports. This
report consists of three sections namely;
1. A ranked list of the best scoring HMMs
2. A list of the best scoring domains in order of their occurrence
in the sequence
3. Alignments for all the best scoring domains.
Section 3 can be truncated to a specific number using the ??A?
option when building the report.
Though the Bio::SearchIO::hmmer module parses through the entire
HMMER report (Section 1, 2 and 3), the set of values made
available through Bio::Search::Result::ResultI seem to be using
Section 3 alone. So when we use the ?A option to truncate, we lose
otherwise useful information in Section 1. This information is
lost (only) for those models that do not have any of their domains
in the top ?A number of? best scoring domains. The fields that are
not available are:
1. Description of a model
2. Score of a model
3. Evalue of a model
If I use the older Bio::Tools::HMMER:Results module, NEITHER
Bio::Tools::HMMER::Domain or Bio::Tools::HMMER::Set allow me to
retrieve the above listed values. Scores and Evalues are available
for each domain but not for the model it belongs to.
I was wondering if there is any other method to access these
values or do I have to write my own module to do this?
Any ideas/suggestions would be greatly appreciated.
Graduate Research Assistant
High Performance Computing Center
University of Florida
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