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Companion Website

Sansom & Horton: Internet for Molecular Biologists

Chapter 04

Free software sources for genome research
Name Type URL
Phred Sequencing base-calling with quality information http://www.genome.washington.edu/UWG C/analysistools/phred.htm
Phrap Sequence assembly http://www.genome.washington.edu/UWG C/analysistools/phrap.htm
Consed Phrap's companion sequence assembly editor http://www.genome.washington.edu/UWGC/analysistools/consed.htm
SWAT and CrossMatch Sequence alignment tools http://www.genome.washington.edu/UWGC/analysistools/swat.htm
TIGR assembler Sequence assembly http://www.tigr.org/softlab/assembler/
StackPACK" Sequence assembly http://www.sanbi.ac.za/CODES/STACKPACK_REQUEST/
Staden package Sequence assembly http://www.mrc-lmb.cam.ac.uk/pubseq/


Other web resources for agricultural biotechnology
Genome databases
ARS-GDR
http://genome-ars.cornell.edu
National Genetic Resources Program (NGRP/Grin) http://www.ars-grin.gov
NCBI http://www.ncbi.nlm.nih.gov
TIGR http://www.tigr.org
Plant genome project websites
Clemson University Genomics Institute
http://www.genome.clemson.edu
International Rice Functional Genomics Working Group http://www.irri.org/genomics
Maize Genome Database http://www.zmdb.iastate.edu
North American Barley Genome Project http://www.css.orst.edu/Barley/nabgmp/nabgmp.htm
Rice Genome Research Project http://rgp.dna.affrc.go.jp
US Wheat Genome Project http://wheat.pw.usda.gov/NSF
Websites for major centers in plant biology
Carnegie Institute of Washington
http://www.ciw.edu
Cold Spring Harbor Laboratory http://www.cshl.org
CIMMYT--International Maize and Wheat Improvement Center http://www.cimmyt.mx
International Rice Research Institute (IRRI) http://www.irri.org
Institute of Plant Genetics and Crop Plant Research http://pgrc.ipk-gatersleben.de
John Innes Centre http://www.jic.bbsrc.ac.uk
Scottish Crop Research Institute (SCRI) http://www.scri.sari.ac.uk
Agricultural biotechnology and GMO-food resources
Biotechnology-an information resource
http://www.nal.usda.gov./bic
Council for Biotechnology Information http://www.whybiotech.com
U.C. Berkeley Outreach http://plantbio.Berkeley.edu/~outreach/
U.C. Davis Biotechnology http://ww.biotech.ucdavis.edu/
Dupont Biotechnology http://www.dupont.com/biotech
Monsanto http://www.monstanto.com
Monsanto--food biotechnology in the UK http://www.monsanto.co.uk
Union of Concerned Scientists http://www.ucsusa.org
Plant biology education websites
American Society of Plant Biologists (ASPB) Education Foundation
http://www.aspb.org/education
Agricultural Library Kids' Science Page http://www.nal.usda.gov/Kids
The Oregon Wolfe Barleys http://www.css.orst.edu/barley/WOLFEBAR/WOLFNEW.HTM
Plant Breeding Updates http://www.dessica.de.pbu
Other plant-related web resources
Curtis Botanical Magazine
http://www.nal.usda.gov/curtis
National Agricultural Library http://www.nal.usda.gov
USDA http://www.usda.gov
USDA plants database http://www.usda.gov/plants
Vascular Plant Image Gallery http:///www.csdl.tamu.edu/FLORA/gallery.htm
Wayne's Word of Unusual and Noteworthy Plants http://waynesword.palomar.edu/worthypl.htm
Link Libraries
National Agricultural Library
Plant Genome Information Resource http://nal.usda.gov/pgdic/
Bioinformatics Resources on the World Wide Web http://sullivan.bu.edu/~mfrith/tools.shtml
The Plant Link Library http://www.dpw.wageningen-ur.nl/links/