Electronic Meeting transcript on "Fast Database Searches

Francisco M. De La Vega fvega at paco.com.mx
Fri Sep 20 15:46:17 EST 1996


Available: Electronic Meeting transcript on "Fast Database Searches
and Evolutionary Relationships Among Proteins", by Dr. W. Pearson.

The latest release of Fasta (v. 3.0) and its appropriate use for fast
database searches was the main topic discussed in the Guest Lecture
delivered by Dr. William Pearson of the Department of Biochemistry
at the University of Virginia, USA, at the electronic conferencing
system BioMOO on June 7th, 1996. Most of the 21 attendants, which came 
from 7 countries, were students of the Summer 1996 BioComputing Course,
a novel distance learning experience organized for the second time
by the BioComputing Division of the Virtual School of Natural Sciences,
a member school of the Globewide Network Academy. The Course covered the
fundamentals of sequence analysis and comparision, was completely
delivered
through the Internet for free and lasted 2 months and a half, attracting
37 participants from all over the world (for an account of the course,
and access to its hypertext book and related materials, visit the URL:
http://www.techfak.uni-bielefeld.de/bcd/welcome.html ).

The edited transcript includes a link to the main FastA v 3.0 FTP
distribution site and to previous lectures, and is available at the 
following locations (WWW/hypertext):
http://www.techfak.uni-bielefeld.de/bcd/Lectures/pearson3.html
http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Lectures/pearson3.html
http://www.biotech.ist.unige.it/bcd/Lectures/pearson3.html

The discussion included an account of the new features incorporated
in version 3.0 of FastA and how it compares with the popular NCBI
BLAST algorithm. The influence of the length of the sequences on the
database similarity scores and how this is corrected in FastA 3.0
was an important point of the talk. A strategy for identifying distant
protein homology during a fast database search, and general tips on the
interpretation of the output of these methods was discussed with the
participants.

The Electronic Conference was organised by the VSNS Biocomputing
Division, sponsored by the Research Group in Practical Computer Science,
University of Bielefeld, and the Association for the Promotion of
Science
and Humanities in Germany (Stifterverband fuer die Deutsche
Wissenschaft).
We would like to thank the Aspen Center for Physics for providing its
facilities for the 1996 "Identifying features in Biological Sequences"
Workshop and the Internet link from which Dr. Pearson and Dr. De La
Vega connected, and to Digital Equipment Corp. for the workstation
cluster provided for the workshop. Alexander Sczyrba, David Atherton, 
Gustavo Glusman, Eric Mercer, and other "BioMOO folks"
(see http://bioinfo.weizmann.ac.il/BioMOO) are thanked for their kind
assistance.

Regards,
Francisco M. De La Vega
Georg Fuellen

GNA-VSNS BioComputing Division





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