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Chapter Two: Genome Sequencing and Annotation—Hyperlinks

• Phred program, University of Washington (page 69):
  http://www.phrap.org/phredphrapconsed.html
• Science Magazine, Functional Genomics, The Human Genome - An Interactive Timeline (page 83):
  http://www.sciencemag.org/feature/plus/sfg/human/timeline1.dtl
• SourceForge, Open Source Software (page 89):
  http://sourceforge.net
• Science Magazine, The Sequence of the Human Genome, paper (page 95):
  www.sciencemag.org/cgi/content/full/291/5507/1304/DC1
• NCBI, Expressed Sequence Tags database (page 96):
  http://www.ncbi.nlm.nih.gov/dbEST
• Ensembl Genome Browser (page 96):
  http://www.ensembl.org
• H-InvDB, Annotated Human Gene Database (page 98):
  http://www.h-invitational.jp
• UCSC Genome Bioinformatics (page 102):
  http://genome.ucsc.edu
• PipMaker (page 103):
  http://bio.cse.psu.edu/
  (Note: The following is a more direct link to the PipMaker page:
  http://pipmaker.bx.psu.edu/pipmaker/
• VISTA (page 103):
  http://www-gsd.lbl.gov/vista
• eShadow software (page 103):
  http://eshadow.dcode.org
• miRBase, microRNA database (page 107):
  http://microrna.sanger.ac.uk
• ENCODE Data Coordination Center at UCSC (page 112):
  http://genome.ucsc.edu/ENCODE
• NCBI, COGs - Clusters of Orthologous Groups of proteins (page 117):
  http://www.ncbi.nlm.nih.gov/COG" target="_blank
• InParanoid, Stockholm Bioinformatics Center (page 119):
  http://inparanoid.sbc.su.se/cgi-bin/index.cgi
• PAUP software (page 120):
  http://paup.csit.fsu.edu
• The Gene Ontology (GO) consortium (pages 124):
  http://www.geneontology.org
• The Gene Ontology (GO) consortium (pages 126):
  http://www.geneontology.org
• Gene Ontology network for plant gene (page 127):
  http://www.geneontology.org/go.nodes.html
  (Note: This address is no longer active; search "plant" at:
  http://www.genenotology.org)
• The Gene Ontology, AmiGO (page 127):
  http://amigo.geneontology.org
• GoSurfer (page 127):
  http://bioinformatics.bioen.uiuc.edu/gosurfer
• PANTHER Classification System (page 128):
  http://www.pantherdb.org

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