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Comparative Bioinformatics -- Links

Course Links

U. Maryland library site for this class: http://www.lib.umd.edu/UMCP/MCK/TUTOR/bioinformatics.html

University of Maryland Biotechnology Institute (UMBI): http://www.umbi.umd.edu

UMBI Computer Resources: http://www.umbi.umd.edu/computing/

Ambiguity codes, abbreviations, and the genetic code

Overview of Biological Diversity


Databases

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

EMBL (European Molecular Biology Lab): http://www.embl-heidelberg.de/

The EMBL Bioinformatics Institute: http://www.ebi.ac.uk/

With an extensive archive of downloadable software: ftp://ftp.ebi.ac.uk//pub/

DNA Data Bank of Japan: http://www.ddbj.nig.ac.jp

Organellar genome project (Canada): http://megasun.bch.umontreal.ca/

Ribosomal Database Project: http://www.cme.msu.edu/RDP

Webcutter: http://firstmarket.com/firstmarket/cutter/

WebGene: http://www.bio.geneseo.edu/~yin/WebGene/WebGene.html

TreeBASE - A database of phylogenetic trees and data matrices published in the primary systematic literature.


Software

Genome Browsers

Ensembl: http://www.ensembl.org

University of California, Santa Cruz: http://genome.cse.ucsc.edu

Contig Assembly and Sequence Analysis

Gene Codes Corporation (Sequencher): http://www.genecodes.com/

Comparative analysis

MacClade Home Page: MacClade Home Page

PAUP Home Page: http://www.lms.si.edu/PAUP/index.html

PHYLIP Home Page

Documentation for PUZZLE 3.0

TreeView


Genomics

National Center for Genome Resources: http://www.ncgr.org/

Genome Sequence Data base: http://www.ncgr.org/research/sequence/

TIGR: http://www.tigr.org

Celera: http://www.celera.com

OU Genomics: http://www.genome.ou.edu/

PHRMA: http://www.phrma.org/genomics/index.html

GenomeWeb links to genomic sites: http://www.hgmp.mrc.ac.uk/GenomeWeb/

DOGS - Database Of Genome Sizes: http://www.cbs.dtu.dk/databases/DOGS/index.html


Taxa

Guides to Taxonomic Information: http://35a-505.umd.edu/taxonomy.html

The Tree of Life Project Root Page

UC Web Lift to Taxa

Extreme eukaryotes (web)

University of California Museum of Paleontology, specifically the Phylogeny of Life pages

Systematic Biology WWW site

Biodiversity and Biological Collections WWW Server

ERIN --Life - Biodiversity

Smithsonian Natural History Home Page

Resources

BCM Search Launcher

BCM Search Launcher: Multiple Sequence Alignments

BLAST PROTEIN AGAINST THE COMPLETE GENOMES

Molecular Biological FTP servers

The Antibody Resource Page

The WWW Virtual Library: Evolution (Biosciences)

The WWW Virtual Library (Biosciences)

MendelWeb Homepage

Dictionary of Cell Biology

Informatics Group

SpliceJunction-logo

RNA secondary structure (Gutell Lab): http://www.rna.icmb.utexas.edu/

Molecular Biology

PCR Jump Station

Protocols on the World Wide Web

Laboratory Protocols List

Technical Tips Online

Perkin Elmer's PCR Technical Tip

Funding Agencies

The National Science Foundation

The National Institutes of Health

Department of Agriculture

 

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