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2 Handbook of Plant Biotechnology: KC012 WL052A June 16, 2003 15:25 Char Count 0

This document provides a table listing URLs and descriptions for various plant genome informatics tools and resources. The table includes over 30 entries describing resources for tasks like sequence databases, analysis software, gene expression databases, protein family signatures, phylogenetic analysis tools, and databases for plant genomes, ESTs, cis-regulatory elements, and non-coding RNAs.

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48 views

2 Handbook of Plant Biotechnology: KC012 WL052A June 16, 2003 15:25 Char Count 0

This document provides a table listing URLs and descriptions for various plant genome informatics tools and resources. The table includes over 30 entries describing resources for tasks like sequence databases, analysis software, gene expression databases, protein family signatures, phylogenetic analysis tools, and databases for plant genomes, ESTs, cis-regulatory elements, and non-coding RNAs.

Uploaded by

rajkumarlodh
Copyright
© © All Rights Reserved
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Download as PDF, TXT or read online on Scribd
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KC012 WL052A June 16, 2003 15:25 Char Count= 0

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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