From: Kann, Maricel (NIH/NLM/NCBI)
Sent: Monday, May 12, 2003 4:20 PM
To: 'ncbi@ncbi.nlm.nih.gov'
Subject: CBB seminar, Tuesday May 13th @ 11AM, 5th f, 38A.

Tuesday, May 13, 11 AM
5th floor conference room, Bldg. 38A

Maricel Kann.
Computational Biology Branch, National Center for Biotechnology Information, NLM, NIH.
BLOCKER: combining structure and function information in a local alignment search tool for sequence-sequence comparison

In this work, we introduce a software package (BLOCKER) that uses a new approach for the placements and penalization of gaps with a novel approach for the definition of aligned regions. This algorithm produces a local alignment between a query protein sequence and a database of PSSMs, and uses a scoring scheme based on the differences in conservation along the protein sequences (conserved domains or CDs). The scores obtained using BLOCKER follow an extreme value distribution which allows the correct estimation of their statistical significance. BLOCKER's performance in the search for biological relationships, alignment accuracy and speed is very similar to IMPALA's. Based on these results, BLOCKER has been successfully included into Cn3D as an alternative choice for the alignment of new sequences. 
A global version of BLOCKER, was also implemented into Cn3D and provides a valuable tool for the alignment of sequences in CDs.