This is a lead in page for the BioInformatics course

This is a lead in page for the BioInformatics course (Biol-473). Those in a hurry to get to the 'short list' of Web resources on this page can follow the links. If you want to get an early start on the problem sets based on the Entrez portal to the databases, start with these exercises. Place this list of queries and your answers in the student drop box and recieve substantial bonus points and a great experience for your self-motivated and self-paced efforts! For those who missed the first night here is an important gene-finding tutorial that we covered and is necessary for the homework for week-1 & 2.

Our threaded discussion board may be used to ask questions about assignments, post your new discoveries of useful web sites, bioinformatic articles and issues of interest or elicit collaborations among the class members.

Dr. McCaman had the pleasure of attending (March 01) another NCBI-sponsered Workshop at the City of Hope Medical Center presented by an old friend Dr. Peter Cooper. Check out the rich learning opportunities afforded by this Field Guide to GenBank and NCBI Resources. The links to problem sets for the Entrez, Blast, Structures and Genomic Resources are mini- bioinformatics courses in themselves!

For March 15 & 22 classes there will be opportunities to become familiar with UNIX systems (see example of unix interactions) and to learn some simple programming techniques using perl scripts. The host computer for these exercises will be codon2.fullerton.edu which you will access using a telnet application and login and password assigned to you individually by the instructor. Some important links to tutorials for these exercises include:

A tutorial prepared by Tae Ryu in CSUF Computer Science department and an external tutorial- http://www.cgi101.com/ (this one has very easy and useful examples for Web applications). Perl 5 by Example is a great book that should be read by anyone seeking to learn Perl and cgi. Fortunately for you it is available over the internet at codebits.com ! Study it carefully and completely including cgi! In addition there will be other simple exercises in class

A searchable database of abbreviations and acronyms in Biotechnology (not my favorite but may do in a pinch- another more limited glossary - can you find a better one to help all of us?

Here is a quick link to MySQL Reference Manual for version 3.23.5-beta at http://linux.cis.nctu.edu.tw/docs/mysql/Manual_chapter/manual_toc.html. for those of you interested in accessing databases on Codon2 (NB the web interface to these databases is under construction-you have to use mascon or secure shell telnet.

Short List of Biol-473 Molecular Links

Links

Entrez Query - Retrieve nucleic acid and/or peptide sequences from GenBank in a variety of formats

TACG- A terrific collection of programs for translation & restriction mapping - thanks to Harry Mangalam, the creator, TACG (ver3) is also on our codon2.

BLAST Search at NCBI

Multiple sequence alignments at European Bioinformatics (EBI) also Clustal provided by web sites at Baylor

ExPASy Molecular Biology Server-the ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB). This server is dedicated to the analysis of protein sequences and structures and with its excellent collection of annotated databases and very useful analytical tools, may be the single BEST web site for doing !!!

PubMed Search NLM's search service to access the 10 million citations in MEDLINE and Pre-MEDLINE (with links to participating on-line journals), and other related databases

BOXSHADE server Take a multiple sequence alignment file (i.e. an alignment file from ClustalW) and produce graphical or color output for slides and prints (also see MSA under Protein Analysis, below)

Educational tutorials at NCBI- Blast, Entrez, OMIM, etc.

Problem Sets at NCBI (for Blast, Entrez, OMIM, etc.)

Field Guide to Genbank & NCBI Resources

Sequence Utilities (BCM): ReadSeq, Primers,6-Frame Translation, Reverse Compliment, etc.

PCR and Primer Design: Tutorial

Gene Finder: Locate splice sites, exons, introns, etc.

Molecular Biology Servers and Databases from SanDiego State

Java Workbench is an interesting set of analyses tools that you can also download to use locally!

Identify transcription factor sites (1 2) in your sequence or download your own software

BioToolKit

Protein Sequence and Motif Databases at U. of Leeds

Prediction ServersTo identify O-glycosylatio and signal peptides and To identify transmembrane regions and various motifs

BLITZ: Find protein sequence similarities or patterns at EMBL.

Institute's (EBI) using ClastalW to identify conserved and consensus sequences among proteins and to explore their evolutionary relationships.

Molecular Modeling: Molecular modeling at NIH. and at Stanford

The Protein Data Bank Brookhaven Protein Data Bank. Retrieve coordinates of various solved structures. View in 3D with appropriate add-in viewers

Informations, Links and News on all aspects of Functional Genomics Research

FreeWare: Dambe, DNA Workbench and others listed in 'mobile' website

Biology WorkBench (SanDiego2000) and some example projects (HIV evol, disease)

Biology WorkBench -SDSC/NCSA

Biology Workbench Investigation Portal (w/ Biology Student Workbench)

KinMutBase: A registry of disease-causing mutations in protein kinase domains

Darwin2000- My favorite molecular-genetics-bioinformatics learning site

Links to the free Science(Celera) and Nature(Public) issues covering various aspects of the "completion" of the human genome project (a must read for all humans even those who are biologists!!!!

free issue of Genome Res. 10 (4) (2000) devoted to genome annotation

Bioinformatics Courses on the Web

bioinformatics glossaries

On Line Journals and Tutorials

New Genomic toy and unusual Viewer (Human Genome Browser)

Australian tools for Bioinformatics

Penultimate collection of esoteric Genomic Tools : Intronerator

For a more comprehensive list see 'Mol-Links on : http://24.0.193.238/mobile

Also use the above site (in /473 or /412 or /nick instead of /mobile) for additional problems along with Darwin2000