Sequence Analysis on the Web

Entry Points and General Resources

This Talk

http://stein.cshl.org/talks/BioWWW/

WWW Virtual Library, Biology Division

A searchable collection biology links maintained by Harvard Biological Laboratories.

http://golgi.harvard.edu/htbin/biopages

WWW Virtual Library, Genetics Subdivision

Links specific to molecular biology and genetics, maintained by Oak Ridge National Laboratory.

http://www.ornl.gov/TechResources/Human_Genome/genetics.html

Biologist's Control Panel

Links to genome centers, genome tools, databases, and analytic tools maintained by Baylor College of Medicine.

http://gc.bcm.tmc.edu:8088/bio/bio_home.html

Pedro's BioMolecular Research Tools

Once a well-maintained list of tools and resources, but not updated since June 1996. Still very useful.

http://www.public.iastate.edu/~pedro/rt_1.html

Got a Name: Get a Sequence

NetEntrez

One-stop shopping for sequences submitted to GenBank. Many search and crossreferene options, maintained by the friendly folk at the NCBI.

http://www.ncbi.nlm.nih.gov/Entrez/

SRS (Sequence Retrieval System)

A massively crossreferenced index of DNA, protein, 3D structure and function databases. Conveniently located in Europe.

http://www.embl-heidelberg.de/srs5/

ENSEMBL (Human rough draft)

http://www.ensembl.org/

The Genome Channel (Human rough draft)

http://compbio.ornl.gov/channel/

Got a Sequence: Get a Name

The one... the only... NCBI BLAST server

Sequence homology searching you can count on. Now in 31 flavors.

http://www.ncbi.nlm.nih.gov/BLAST/

Sanger Centre: H. sapiens, S. cerevisiae, S. pombe, C. elegans, P. falciparum, M. leprae....

Multiple organisms in various stages of sequencing at the Sanger Center.

http://www.sanger.ac.uk/DataSearch/

Washington University: C elegans, C. briggsae, A. thaliana, H. sapiens

Multiple organisms in various stages of sequencing at Wash U.

http://genome.wustl.edu/gsc/gschmpg.html

Stanford: A. thaliana

BLAST server for various Arabidopsis extracts from GenBank.

http://genome-www2.stanford.edu/cgi-bin/AtDB/nph-blast2atdb

Others

Check the Web pages of the genome center(s) working on the organism you're interested in.

Got a Sequence: What Does it Do?

GRAIL

Exon prediction, polyAdenylation sites, simple repeats and CpG islands and more. The power of a supercomputer at your back and call... when it's working.

http://compbio.ornl.gov/Grail-1.3/

GeneFinder

An alternative exon prediction program, with models tuned for human, drosophila, nematode, yeast and plant genes. Maintained by Baylor.

http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html

BCM Search Launcher

The page that launched a thousand scripts. Run BLAST searches, gene prediction programs, protein secondary structure prediction, and multiple alignments in batch mode. Also available as a Perl script that runs on Macs, Windows and Unix machines.

http://kiwi.bcm.tmc.edu:8088/search-launcher/launcher.html

NCSA Biologist's Workbench

A large collection of sequence and protein analysis tools, designed for interactive use.

http://biology.ncsa.uiuc.edu/

PRIMER3

Automated PCR primer picking at the Whitehead Institute's Web site.

http://www.genome.wi.mit.edu/cgi-bin/primer/primer3.cgi

Online Mendelian Inheritance in Man

The definitive guide to known human genes, diseases, and phenotypes. Now integrated into Net Entrez.

http://www3.ncbi.nlm.nih.gov/Omim/

Got a Sequence: Where Does it Live?

ENSEMBL (Human rough draft)

http://www.ensembl.org/

Entrez, Genomes Division

Various groups' maps of various organisms, displayed in "BogoBase" units.

http://www3.ncbi.nlm.nih.gov/Entrez/Genome/org.html

Human Gene Map

UniGene clusters placed on a radiation hybrid map by an international cabal.

http://www3.ncbi.nlm.nih.gov/SCIENCE96/

Whitehead Institute Human and Mouse Maps

Whole genome maps using a variety of genetic and physical mapping techniques.

http://www.genome.wi.mit.edu/

Stanford University Human Map

A high resolution radiation hybrid map of the human genome.

http://shgc.stanford.edu/

FlyBase

Drosophila maps (and other information) maintained by University of Indiana.

http://flybase.bio.indiana.edu/

MGD (Mouse Genome Database)

Definitive repository of mouse mapping information, maintained by Jackson Laboratory.

http://www.jax.org/

SGD (Saccharomyces Genome Database)

Maps of baker's yeast, maintained at Stanford.

http://genome-www.stanford.edu/Saccharomyces/

TIGR

A well-organized database of various microbial genomes, maintained at The Institute for Genome Research.

http://www.tigr.org/

WormBase

An online C. elegans database maintained at CSHL

http://www.wormbase.org

AtDB

An online A. thaliana database, maintained at Stanford.

http://genome-www.stanford.edu/Arabidopsis/

Proteome Databases

Yeast and Worm databases, organized in "protein centric" fashion

http://www.proteome.com

Got a Sequence: Who Got there Before You?

PubMed

Bibliographic retrieval system, maintained by NCBI. Well-integrated into net Entrez.

http://www.ncbi.nlm.nih.gov/PubMed/