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2 HANDBOOK OF PLANT BIOTECHNOLOGY

Table 4.1 URLs for plant genome informatics tools and resources discussed in this chapter

Resource URL Description

AtRepBase nucleus.cshl.org/protarab/AtRepBase.htm Repeat sequences in Arabidopsis

BioMail www.biomail.org/ Pubmed search robot
BLOCKS blocks.fhcrc.org/ Protein family alignments
Comprehensive Microbial Resource www.tigr.org/tdb/mdb/mdbcomplete.html Microbial genomes and analysis tools
DDBJ www.ddbj.nig.ac.jp/ Primary sequence database
Distributed Annotation System www.biodas.org Software for managing genome
sequence data
EMBL Nucleotide Sequence www.ebi.ac.uk/embl/index.html Primary sequence database
Database
EMBOSS www.emboss.org/ Sequence analysis software
Enzyme Commission Database www.expasy.ch/enzyme/ Enzyme nomenclature
Genbank www.ncbi.nlm.nih.gov/Genbank/index.html Primary sequence database
Gene Expression Omnibus (GEO) www.ncbi.nlm.nih.gov/geo/ Gene expression database
Gene Indices www.tigr.org/tdb/tgi.shtml Non-redundant gene sets
for many organisms
Gene Ontology Consortium www.geneontology.org/ Controlled vocabulary
for gene function
GeneNet www.mgs.bionet.nsc.ru/mgs/systems/genenet/ Gene network data and analysis tools.
GOBASE megasun.bch.umontreal.ca/gobase/ Organelle genome database
gobase.html
GOLD igweb.integratedgenomics.com/GOLD/ Information about genome projects
eukaryagenomes.html
Graingenes wheat.pw.usda.gov/index.shtml Genomic database for wheat, oat,
barley, rye and sugarcane
Gramene www.gramene.org/ Comparative genome analysis
in the grasses
HMMer hmmer.wustl.edu/ Profile hidden Markov model software
HYPHY peppercat.stat.ncsu.edu/∼hyphy Software for analysis of
sequence evolution
Indiana University iubio.bio.indiana.edu/soft/molbio/ Bioinformatics Software
Molecular Biology
Software Archive
InterPro www.ebi.ac.uk/interpro/ Integrated database of protein
family signatures
Klotho www.ibc.wustl.edu/klotho/ Biological compound database
MaizedB www.agron.missouri.edu/ Maize genomics
Mendel Plant Gene Names genome-www.stanford.edu/Mendel/ Nomenclature for sequenced
aboutMendel.html plant genes
MIAME www.mged.org/Workgroups/MIAME/ Microarray annotations
miame.html working group
MMDB www.ncbi.nlm.nih.gov/Structure/ 3D-biomolecular structures
PAML abacus.gene.ucl.ac.uk/software/paml.html Software for analysis of sequence
evolution
PDB www.rcsb.org/pdb/ Primary structural database
Pfam www.sanger.ac.uk/Software/Pfam/ Protein family signatures
PHYLIP evolution.genetics.washington.edu/phylip.html Software for phylogenetics
Phylodendron iubio.bio.indiana.edu/treeapp/ Software for drawing phylogenetic trees
PLACE www.dna.affrc.go.jp/htdocs/PLACE/ Plant cis-acting regulatory elements
Plant Genomes Central www.ncbi.nlm.nih.gov/PMGifs/Genomes/ Plant genomics database
PlantList.html
PlantCARE sphinx.rug.ac.be:8080/PlantCARE/cgi/ Plant cis-acting regulatory elements
index.html
PlantGDB www.zmdb.iastate.edu/PlantGDB/ Plant ESTs and comparative gene
modelling
PLANTncRNAs www.prl.msu.edu/PLANTncRNAs/ Plant non-protein coding RNAs
Primer3 www-genome.wi.mit.edu/cgi-bin/primer/ Primer design
primer3 www.cgi

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