[Bioperl-l] Bio::SearchIO - Accessing Model parameters (score, evalue, description)

Kadirvel, Selvi 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.

Thank you!

Selvi Kadirvel

Graduate Research Assistant
High Performance Computing Center
University of Florida

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