National Science Foundation | Pine/Conifer Genome Databases | General Pine/Gymnosperm Sites | Molecular Resource Distributors | Taxonomic Resources | Sequence Databases | Other Plant Genome Databases | Conference Websites | Genomics Tools | Journals | Governmental Agencies | Computational Resources | General Molecular Databases

National Science Foundation (NSF)

Division of Biological Infrastructure (DBI)

Molecular Resource Distributors

  EST - expressed sequence tags
  GSS - genome survey sequences
  STS - sequence tagged sites
  SNP - single nucleotide polymorphisms
  Entrez - NCBI's search and retrieval system
  structure - 3-D macromolecular structures
  genome - whole genomes of over 800 organisms
  protein - protein entries from SwissProt, PIR, PRF, PDB
  nucleotide - nucleotide entries from GenBank
  PubMed - NCBI's literature DB
  taxonomy - taxonomic system used by NCBI
EMBL- Europe's primary nucleotide sequence resource
DDBJ - DNA Data Bank of Japan
VectorDB - A vector sequence DB

General Molecular Databases

ChromDB  - plant chromatin database.
Codon Usage Database- a large list of organisms available
Gene Ontology Consortium

Plant DNA C-values Database

PLACE  - DB of plant cis-acting regulatory DNA elements
PlantsP  - functional genomics DB of plant phosphorylation
Signaling Pathway Database (SPAD)  - genetic information and signal transduction

Transcription Regulatory Regions Database - transcription factor binding sites, promoters, enhancers, silencers, etc.
Transterm  - messenger RNA components and signals

JGI Poplar Genome Portal - Poplar genome sequence

Click here for Arabidopsis, rice, maize, sorghum, and cotton DB links

Other Genomics Resources

ATGpr - prediction of translation start sites in cDNA sequences

Baylor College of Medicine Sequence Analysis
bend.it - calculate curvature and bendability of a DNA sequence

BioWeb Pasteur - biological software from the Pasteur Institute
CBS Prediction Servers - prediction of protein subcellular localization and various sites in protein and nucleotide sequences
CMS Resource - sequence analysis tools
Compute pI/Mw Tool
CpG Islands - predict CpG islands

EST parser - find alternative polyadenylation sites in mRNAs, using ESTs

Eukaryotic Promoter Database (EPD) - an annotated, non-redundant collection of eukaryotic Pol II promoters
ExPASy Proteomics Tools
FGENES-H - a powerful ab initio gene prediction program used in sequence analysis of the rice genome
FPC V6 and WebFPC V1.3
GeneMark.hmm - a shareware gene analysis program developed by Georgia Tech

GENSCAN - a widely-used MIT gene search and analysis tool
Glimmer - gene finder for Arabidopsis and rice genomic sequence
GlimmerM - find and analyze eukaryotic gene sequences
Image - fingerprint image analysis system
Melting - calculate melting temperature for nucleic acid duplexes

mfold - RNA secondary structure prediction

NetStart - prediction of translation start sites in vertebrate and A. thaliana sequences

NSITE-PL - a program that facilitates recognition of plant regulatory motifs

Phred/Phrap/Consed System Home Page
Plant Cis-acting Regulatory DNA Elements (PLACE) - a database of motifs found in plant cis-acting regulatory DNA elements
Primer3 - primer design

Promoter Scan - an  NIH program that predicts promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences
PSORT - prediction of protein sorting signals and transmembrane helices

Queen's University Online Analysis Tools
Repeatmasker - mask repetitive elements in DNA sequences

Reverse complement nucleotide sequences
SignalP - secretory signal peptide prediction

Tandem Repeats Finder

TIGR genomics tools - a large collection of freely available software tools

Translate Tool
TSSP - a program that aids in discovery of plant promoters
UTR-extender - extends missing ends of an mRNA using EST and genome sequence data
Vienna RNA Package - RNA secondary structure prediction
webcutter - detect restriction enzyme cutting sites in DNA sequences

Computational Resources
Alphabetical Directory of Linux Commands

Apache web server documentation
bioperl - bioinformatics related PERL modules
biopython - freely available Python tools
C++ Annotations
C++ Standard Template Library Programmer's Guide
CPAN - PERL modules
C Tutorial
Dictionary of Algorithms, Data Structures, and Problems
Dinkum C Library Reference
GNU C Library Reference
HTML Writers Guild
Java Tutorial
Numerical Recipes in C and Fortran
PHP information
The Linux Cookbook
W3C - WWW Consortium, the definitive HTML reference