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 Arabidopsis
Maize
Rice
Cotton
Sorghum
Sequence Databases
Germplasm Databases & Repositories
Genomics Centers & Institutes
Bioinformatics
Comparative Mapping
Genomics Tools
Computational Resources
Microarrays
Proteomics
Physical Mapping
Journals/Techniques/Articles
Web Software
Genetic and Physical Mapping Databases
Motif and pattern finding
Phylogeny & Taxonomy
Gene-finding software
Pathways
Miscellany |
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| Arabidopsis |
MATDB - searchable index and visualization of positional information for BAC clones and single genes
TIGR Arabidopsis Database
Arabidopsis Functional Genomics Consortium (AFGC)
Plant Plasma Membrane Database (PPMdb) - Arabidopsis plasma membrane proteins with expression and sequence data
Arabidopsis Genomics, TAIR
Plant Plasma Membrane Database (PPMdb) - A. thaliana plasma membrane proteins with expression and sequence data
AtDB (TAIR)- genetic/physical mapping data
Arabidopsis thaliana chromosomes 4 & 5 - genetic/physical maps
The Arabidopsis Information Resource
Arabidopsis cDNA Sequence Analysis Project
The Arabidopsis Genome Center (ATGC)
Everything Arabidopsis
The TIGR Arabidopsis Database Project |
| Maize |
MaizeGDB
Maize links (Maize Co-op at the University of Missouri) |
| Rice |
Rice Genome Database (Beijing Genomics Institute)
Rice Genome Project (Syngenta)
TIGR Rice Annotation and Informatics
Rice Genome Research Program |
| Cotton |
Cotton Genome Center at U. C. Davis
CottonDB - a genome database for Gossypium |
| Sorghum |
Comparative Grass Genomics Center - University of Georgia
Sorghum Genomics Project - Texas A & M
Sorghum DB Data Collection Site |
| Sequence Databases |
Genbank
dbEST - expressed sequence tags
dbGSS - genome survey sequences
dbSTS - sequence tagged sites
dbSNP - single nucleotide polymorphisms
Entrez - NCBI's search and retrieval system
structure - 3-D macromolecular structures for proteins and polynucleotides
genome - whole genomes of over 800 organisms
protein - protein entries from SwissProt, PIR, PRF, PDB
nucleotide - nucleotide entries from GenBank
Pubmed
taxonomy - names of all organisms that are represented in the genetic databases
EMBL- Europe's primary nucleotide sequence resource
DDBJ - DNA Data Bank of Japan (sole DNA data bank in Japan)
VectorDB - Molecular Biology Vector Sequence Database |
| Germplasm Databases/Repositories |
The Germplasm Resources Information Network (GRIN)
National Plant Germplasm System (NPGS)
GRIN's list of related sites American
American Type Culture Collection (ATCC)
Plant Virology
Plant Tissue Cultures
Plant Seeds
Fungi and Yeasts
Bacteria
Molecular Biology |
| Genomics Centers & Institutes |
Cold Spring Harbor Laboratory
Genome Sequencing Center
University of Washington Genome Center
The Institute for Genomic Research
The Plant Genome Initiative at Rutgers
Comparative Grass Genomics Center at the University of Georgia
Clemson University Genomics Institute
Arizona Genomics Institute and Computational Laboratory
The Whitehead Institute for Biomedical Research/MIT Center for Genome Research
Institute for Plant Genomics and Biotechnology at Texas A & M
The Sanger Center |
| Bioinformatics |
TIGR Rice Annotation & Informatics
Comprehensive Online Bioinformatics Service (BioNavigator.com) |
| Comparative Mapping |
GenomePixelizer - powerful genome visualization tool
TIGR Brassica Comparative Genomics |
| Genomics Tools |
TIGR genomics tools - a large collection of freely available software tools
Glimmer - gene finder for Arabidopsis and rice genomic sequence
BioWeb Pasteur - biological software from the Pasteur Institute
Queen's University Online Analysis Tools
Baylor College of Medicine Sequence Analysis
ExPASy Proteomics Tools
The CMS Resource - sequence analysis tools
FPC V6 and WebFPC V1.3
The Phred/Phrap/Consed System Home Page
Image - fingerprint image analysis system |
| Computational Resources |
W3C - World Wide Web Consortium, the definitive HTML reference
Apache web server documentation
PHP information
HTML Writers Guild
CPAN - PERL modules
bioperl - bioinformatics related PERL modules
biopython - freely available Python tools for computational molecular biology
C++ Standard Template Library Programmer's Guide
C++ Annotations
Dinkum C Library Reference
GNU C Library Reference
C Tutorial
Java Tutorial
Numerical Recipes in C and Fortran
Dictionary of Algorithms, Data Structures, and Problems
The Linux Cookbook
Alphabetical Directory of Linux Commands |
| Microarrays |
Arabidopsis
TIGR microarray resources
WWW Virtual Library plant arrays |
| Proteomics |
The Protein Data Bank - 3D Molecular data
The Database of Interacting Proteins (DIP) - catalog of experimentally determined interactions between proteins
The Protein Information Resource (PIR) - a
database of sequences, functional, and structural information
to support genomics and proteomics research
ExPASy Proteomics Tools |
| Physical Mapping |
| Texas A&M GENEfinder Genomic Resources - BAC resources for several plant species |
| Journals/Techniques/Articles |
American Journal of Botany
American Journal of Enology and Viticulture
Annals of Botany
BioTechniques
Chromosoma
Chromosome Research
Cell
Current Protocols Online
Frontiers in Bioscience - links to biology newsgroups and protocols
Genes and Development
Genetics
Genome
Genome Biology
Genome Research
Genome Technology
Journal of Agricultural Genomics
Journal of Theoretical Biology
Molecular Biology Protocols
Molecular Breeding
Molecular Genetics and Genomics
National Plant Genome Initiative
Nature
Nature Genetics
New Phytologist
Nucleic Acids Research
Pasteur Institute
Plant Cell
Plant Genome Data and Information Center
Plant Molecular Biology Reporter
Plant Physiology
Proceedings of the National Academy of Sciences
Science
The Plant Journal
The Scientist
Theoretical and Applied Genetics
Trends in Biotechnology
Trends In Genetics
Trends in Plant Science |
| Web Software |
Phylogeny Software - 194 phylogeny packages, 16 free servers
Quantitative Genetics Resources
Biology WorkBench - search many popular protein and nucleic acid sequence databases |
| Genetic and Physical Mapping Databases |
CMS list of plant databases
USDA list of plant databases
BAC centre at Texas A&M - BAC libraries for most of the important plant species
Canadian Bioinformatics Resource
Japan - Database of Research Tools
Japan - GenomeNet
Japan - Genomics Databases
AtDB (TAIR) (Arabidopsis thaliana: thale cress)
BeanGenes (Phaseolus, Vigna spp.: common bean, tepary bean, cowpea, mungbean etc.)
BrassicaDB (B. rapa, B. oleracea and B. nigra)
GrainGenes (Triticum and Aegilops spp. and Saccharum : wheat, barley, oats, rye, and sugarcane)
MaizeDB (Zea maize: corn)
Rice Genome Research Program (Oryza sativa: rice)
Soybase (Glycine max: soybean)
The Institute for Genomic Research Databases (TIGR)
Thale Cress (Arabidopisis thaliana)
Rice (Oryza sativa)
Potato (Solanum tuberosum) |
| Motif and Pattern Finding |
Gibbs Motif Sampler
AlignACE Homepage - gene regulatory motif finding
MEME - motif discovery and search in protein and DNA sequences
SAM - tools for creating and using Hidden Markov Models
Pratt - discover patterns in unaligned protein sequences |
| Phylogeny & Taxonomy |
Species 2000 - index of the world's known species
The Tree of Life
TreeBASE - database of phylogenetic knowledge
PHYLIP - package of programs for inferring phylogenies
TreeView - user friendly tree displaying for Macs & Windows
Computer Programs for Molecular Evolutionary Analysis - includes ADAPTSITE, a program which detects positive and negative selection at single codon sites |
| Pathways |
Network/pathway reconstruction and analysis
BioCyc Knowledge Library - collection of pathway/genome databases. |
| Gene-finding software |
GENSCAN - a widely-used MIT gene search and analysis tool
GlimmerM - find and analyze eukaryotic gene sequences
GeneMark.hmm - a shareware gene analysis program developed by Georgia Tech
Eukaryotic Promoter Database (EPD) - an annotated, non-redundant collection of eukaryotic Pol II promoters
Plant Cis-acting Regulatory DNA Elements (PLACE) - a database of motifs found in plant cis-acting regulatory DNA elements
Promoter Scan - an NIH program that predicts promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences
FGENES-H - a powerful ab initio gene prediction program used in sequence analysis of the rice genome
TSSP - a program that aids in discovery of plant promoters
NSITE-PL - a program that facilitates recognition of plant regulatory motifs |
| Miscellany |
databases:
Transcription Regulatory Regions Database - transcription factor binding sites, promoters, enhancers, silencers, etc.
codon usage database- a large list of organisms available
Transterm - messenger RNA components and signals
The Signaling Pathway Database (SPAD) - genetic information and signal transduction
ChromDB - plant chromatin database.
PlantsP - functional genomics database of plant phosphorylation.
PLACE - database of plant cis-acting regulatory DNA elements.
Plant DNA C-values Database
tools:
Repeatmasker - mask repetitive elements in DNA sequences
Tandem Repeats Finder
Vienna RNA Package - RNA secondary structure prediction
mfold- RNA secondary structure prediction
EST parser - find alternative polyadenylation sites in mRNAs, using ESTs
UTR-extender - extends missing ends of an mRNA using EST and genome sequence data
CpG Islands - predict CpG islands
NetStart - prediction of translation start sites in vertebrate and A.thaliana sequences
ATGpr - prediction of translation start sites in cDNA sequences
SignalP - secretory signal peptide prediction
PSORT- prediction of protein sorting signals and transmembrane helices
CBS Prediction Servers - prediction of protein subcellular localization and various sites in protein and nucleotide sequences
Compute pI/Mw Tool
Translate Tool
Reverse complement nucleotide sequences
Melting - calculate melting temperature for nucleic acid duplexes
bend.it - calculate curvature and bendability of a DNA sequence
webcutter - detect restriction enzyme cutting sites in DNA sequences
Primer3 - primer design |
