DNA Homology Searches

• Search Genbank using BLAST at NCBI
• BLAST using BCM Launcher or BLAST at GenomeNet in Japan
• FASTA at the DNA Databank of Japan
• TAIR FASTA Search of the Arabidopsis Database 
• MPsrch searches sequences in protein and DNA databases for similarity to the query sequence. Queries can include stop codons. (most sensitive sequence comparison method currently available)
• Frame - ProfileScan Search a short DNA sequence against a protein profile database (Prosite) 

Gene Feature Predictions

General 

• Gene Feature Searches including exon and splice site predictions, transcription factor binding sites,  etc. using the BCM Search Launcher
• GRAIL-EXP is a software package that predicts exons, genes, promoters, polyAs, CpG islands, EST similarities, and repetitive elements within DNA sequence.
• RiceGAAS is a rice genome automated annotation system. This system integrates gene-prediction programs and database searches.

Intron/Exon Predictions

• Genie is a Gene Finder Program that uses the Hidden Markov Model to find genes.
• GenScan has been adapted to predict genes in DNA sequences from different organisms including plants
• GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Matrices.

Splice Site Predictions

• NetGene2 predicts splice sites in DNA from human, C. elegans and Arabidopsis.
• NNSSP splice site prediction by neural network
• SliceView Splice Prediction by using Consensus Sequences

PolyA -Site Prediction

• HCPolyA -  Poly A prediction in eukaryotic genes

Open Reading Frame Predictions

• ORF Finder at NCBI
• Six frame translation of DNA sequence into protein
• Formatted DNA sequence translation
• NetStart produces neural network predictions of translation start in vertebrate and Arabidopsis thaliana nucleotide sequence. Has been trained on cDNAs.

Promoter, Transcriptional Factor and TATA signal prediction

• MatInspector Search Sequence for Transcription Factor Binding Sites
• Signal Scan - Search Search for Eukaryotic Transcriptional Elements
• Transcription Element Search System (TESS)
• NNPP Prediction of Promoter using neural network
• BIMAS Promoter Scan predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences
• Tfsitescan analyses promoters
• HcTATA TATA signal prediction
• Plant CARE, Plant Cis-Acting Regulatory Element database, searchable
• PLACE A Database of Plant Cis-acting Regulatory DNA Elements, covering vascular plants.

Repetitive DNA

• CENSOR allows users to have query sequences aligned against a reference collection of human, rodent, or plant repeats. Censoring means replacing the aligned portions with x's in the query sequences.
• GRAIL CpG Isle, Repetitive DNA prediction/Analysis
• RepeatMasker screens DNA sequences in fasta format against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions.
• The REPuter program family provides state of the art software solutions to compute and visualize repeats in whole genomes or chromosomes.
  

MAR - Matrix Attachment Regions

• S/MAR Database collects information about scaffold/matrix attached regions and the nuclear matrix proteins
• SMART test, search for S/Mars at Genomatixs
• Search your sequence using the MAR-Wiz Tool - you will have to register first.

Plant Genome Databases

• Gramene
• IPK Gatersleben / Plant Genome Resource Center
• GrainGenes: A Database for Small Grains and Sugarcane
• UK CropNet, Barley project page
• ITEC: International Triticeae EST Cooperative
• CU Genomics Institute: Clemson University's Barley Homepage
• MaizeDB -- Maize Genome Database
• INRA Maize Genome Database
• ZmDB the Maize Genome Database in Iowa; allows access to EST data
• Korean Rice Genome Database
• Rice Genome Research Project  in Japan
• Syngenta's Rice Genome Project
• Genome database of Oryza sativa L. ssp. indica (Beijing Genomics Institute)
• Medicago Genome Initiative
• TIGR Databases - The Institute for Genomic Research
• TAIR  The Arabidopsis Information Resource
• Cotton Database
• Solanaceae Genomics Network

Plant Organelle Sequences

• Complete Mitochondrial plasmid genome sequences
• Complete Chloroplast genome sequences

Plant Pathogen and other Databases

• Plant Viruses Online
• PhytoPaths is a database of plant-microbe interactions and the genomes involved.
• Neurospora crassa Genome Project
• PLANT-TRRD Plant Transcription Regulatory Regions Database contains information on structural and functional organisation of transcription regulatory regions of eukaryotic genes.
• Phytophtora Genome Consortium Database
• R-Genes: Plant Disease Resistance Genes NCGR's R-Genes project is an investigation of the diversity of plant disease resistance genes (r-genes) and their homologs in genome sequence databases.
• Angiosperm DNA C-Values Database 
• Schizosaccharomyces pombe Genome Database
• Saccharomyces cerevisae Genome Database
  

On Microarrays

• GRID IT: Resources for Microarray Research
• Gene Chips (DNA Microarrays)- Information, references and links
• Stanford Genomic Resources Microarray Database and other links
• MicroArrays (Michael Eisen's lab) 
• Big MicroArray link page

Plant Tissue Culture & Transformation

• Plant Tissue Culture Information Exchange
• Plant Tissue Culture List Server
• Protocols at the Oklahoma Plant Transformation Facility 
  

Methods & Protocols

• Molecular Biology Protocols. Comprehensive site with lots of  techniques, protocols and links.
• Cell and Molecular biology research protocols 
• Standard Plant Molecular Biology Protocols
• Arabidopsis Protocols - The complete guide
• Laboratory Protocol List

Web-based Sequence Manipulation Tools

PCR-Primer Design

• DoPrimer You can either manually paste in a DNA sequence or search the EMBL database for the entry you want and automatically launch the DoPrimer software to analyze it.
• Primer3 Primer design tool which allows you to set many parameters.
• Check out the Alkami Biosystems Page for further information on PCR primers and methods.
• Codehop (COnsensus-DEgenerate Hybrid Oligonucleotide Primers) PCR primers designed from protein multiple sequence alignments

Restriction enzymes

• Webcutter2 Online program that restriction maps DNA sequences
• WWWtacg Restriction Enzyme tool with several other features

ORF &Translate

• Six Frame Translation of Sequence
• ORF Finder at NCBI
• Molecular Toolkit: Translate a DNA sequence and obtain graphical and textual depictions of possible translations

Multiple Sequence Alignment

• Multiple Sequence Alignment using BCM Launcher
• MultAlign Multiple sequence alignment with hierarchical clustering
• CLUSTLW Server at EMBL-EBI  

Free Software

• Chromas is a Windows application which displays and prints chromatogram files from ABI automated DNA sequencers
• BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000. Allows alignments, manipulation and viewing of sequences. Includes fully-automated links to local and WWW-based analysis programs.
• Stanford ABI Viewer is a java application that displays ABI file content including processed and raw chromatograms and other data arrays, comments and labels.

General:

• Genamics SoftwareSeek is a repository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry. Windows, MS-DOS, Mac, Unix and Linux platforms are supported, as well as online tools that run through your internet browser.
• Check out the Biocatalog, a software directory for molecular biology and genetics, at EBI.