Subject: RE: CLL:bioinformatics group?

From: [email-masked] (Phil Xiang)
Date: Sat, 29 Jun 96 13:26:22 -0400

>>Does any body know if there is an internet discussion group for bioinformatics?

>What area of bioinformatics are you interested in??
>
>Michael N. Liebman, Ph. D.
>Director, Bioinformatics
>Vysis, Inc.
>3100 Woodcreek Drive
>Downers Grove, Illinois 60515
>
>(708) 271-7190 office         area code will become 630 on August 1
>(708) 271-7008 fax
>*************************************
>please note new e-mail address   [email-masked]
>*************************************

Bioinformatics is computation for the purpose of constructing and interpreting
genome. As a subdiscipline of biology, it contributes to the understanding of
life by intimate interactions with all other subdisciplines of biology, 
including genetics, molecular biology, structural biology, biochemistry. 

The first logical task of bioinformatics is to construct the entire physical 
map of a genome from pieces called the EST, in a procedure known as genome 
mapping. The main purpose here is to organize the immense amount of data and to
avoid repetitive work.

The second task of bioinformatics is to identify genes, or exons, from the
noncoding parts, or introns. This is possible based on the belief that genes
are subject to constraints during evolution and should therefore have features
different from noncoding regions which are not subject to evolutionary
constraints.

The third task is to tell the function of a gene from its sequence and to 
predict how mutations affect function. It is believed that functionally 
related proteins either evolve 
from common ancesters or have converged during evolution so that they share 
common features in either sequence or structure. The common approaches to
discovering sequence similarities are: homology search, pattern/motif
search, amino acid composition analysis. The common approaches to discovering
structural similarities are: secondary structure prediction, structural
classification, inverse folding (threading, fold recognition), multiple 
alignment, homology modeling.

The forth task is to understand how a set of genes work in concert at the
organismal level. The purpose here is to understand at a quantitative level
processes such as expression/controll/regulation, signal transduction,
biochemical pathways, development, adaptation, evolution. This is the most
exciting part of bioinformatics and my understanding is that the work has
just begun. 

Concepts/Algorithms: physical map, ORF, intron/exon, homology, fold classes,
dynamic programming, Smith-Waterman/Needleman-Wunsch, threading, 3D profiles,
knowledge-based potentials, secondary structure prediction, fold recognition,
pattern/motif, scoring matrices, alignment, Z score, twilight zone, 
phylogenetic tree, neural nets, genetic algorithm.

Databases: GenBank, SwissProt, PIR, PDB, EMBL, GDB, ProSite, ProDom, SCOP,
HSSP/FSSP, ExPASY.

Programs: GeneFind, GCG, BLAST, FASTA, Entrez, OWL, Pileup, ProfileSearch,
CLUSTAL.

Computer tools: Relational database, SQL, Sybase, Oracle, C/C++, Client/Server,
distributed computing, HTML/WWW, cgi, Java, Perl.

The above delineation no doubt reflects my biases and may have missed some 
major marks and as such is only intended to serve as a lead for discussion. 
I am very interested in hearing other points of view. I am especially 
interested in hearing from industry people what skills/talents are hot there.

			Phil Xiang

			Biophysics,Brandeis University,(617)736-4906
			http://www.rose.brandeis.edu:80/users/xiang/