Web-based Tool

Function

Website

GRAMENE Multi BlastView

Verifying the location of primers in rice genome

http://www.gramene.org/Multi/blastview

GRAMENE QTL

Finding more information about a particular trait/QTL

http://www.gramene.org/qtl/

GRAMENE CMap

Finding the location of a marker in a genome; finding more markers for fine-mapping

http://www.gramene.org/cmap/

GRAMENE MapView

Getting a list of predicted genes within a QTL region

http://www.gramene.org/Oryza_sativa_japonica/ index.html

Google

Searching for a new bioinformatics tool

www.google.com

BlastDigester

Generation of CAPS markers

http://www.bar.utoronto.ca/ntools/cgi-bin/ntools_blast_digester.cgi

REBASE

Finding the recognition sequence of a restriction enzyme

http://rebase.neb.com/rebase/rebase.html

NCBI

Retrieving protein and DNA sequences

www.ncbi.nlm.nih.gov. 

CDART

Finding the functional domain of a protein

http://www.ncbi.nlm.nih.gov/Structure/ lexington/lexington.cgi?cmd=rps

Sequence Extractor

Help build DNA construct

http://www.bioinformatics.org/seqext/

Weight to Molar Quantity

Calculation of molar quantity for nucleic acids

http://molbiol.ru/eng/scripts/01_07.html .

Dilution calculation

Dilution calculation

http://www.restrictionmapper.org/ dilutioncalc9.htm

GenBank Feature Extractor

Extracting features from a GenBank entry

http://www.sanbi.ac.za/%7Ermuller/SMS/ index.html

GenBank to FASTA

GenBank to FASTA format

http://www.bioinformatics.org/sms/

lettercount

Counting the number of sequences

http://www.lettercount.com/

Alignment of two DNA, RNA or protein sequences.

Aligning two DNA, RNA or protein sequences

http://insilico.ehu.es/align/

PlasMapper

Plasmid annotation

http://wishart.biology.ualberta.ca/PlasMapper/ index.html

NCBI

Knowing more about viral genomes

http://www.ncbi.nlm.nih.gov/genomes/ static/vis.html

NCBI

Finding more about bacterial genomes

http://www.ncbi.nlm.nih.gov/genomes/ static/eub.html

Swiss-Prot/TrEMBL

Building a phylogenetic tree

http://www.expasy.ch/sprot/ sprot-retrieve-list.html.

PSIPRED

Predicting the secondary structure of proteins

www.bioinf.cs.ucl.ac.uk/psipred

BLAST 2 SEQUENCES

Aligning two nucleotide or protein sequences using BLAST2 sequences

http://www.ncbi.nlm.nih.gov/blast/bl2seq/ wblast2.cgi