Web-based Tool

Function

Website

NCBI PubMed

Finding out more about a protein, a gene, QTL or a trait etc.

www.ncbi.nlm.nih.gov/entrez/

NCBI BLAST

Establishing the identity of a gene, expressed sequence tags (ESTs), or protein by a homology search; sequence comparison; data mining; verifying if sequence is from species of interest; verifying if primers will not anneal to any fungal or bacterial sequences, or any sequences from unwanted organisms

http://www.ncbi.nlm.nih.gov/BLAST/

NCBI Nucleotide

Downloading multiple sequences

http://www.ncbi.nlm.nih.gov/

CLUSTALW

Aligning multiple sequences to detect polymorphisms due to SNP, indels etc.

http://align.genome.jp/

CAP3 Sequence Assembly Program

Assembling sequence fragments to obtain a longer picture of the gene

http://pbil.univ-lyon1.fr/cap3.php

EST2GENOME

Looking for intron-exon junction

http://bioweb.pasteur.fr/seqanal/interfaces/ est2genome.html

Homology Search

Predicting the function of a DNA sequence

http://gibk26.bse.kyutech.ac.jp/jouhou/ HOMOLOGY/dbsearch/

Predotar

Establishing presence of targeting sequences from mitochondria or chloroplast

http://ihg.gsf.de/ihg/mitoprot.html

NCBI Taxonomy Browser

Finding out the taxonomical hierarchy of an organism

http://www.ncbi.nlm.nih.gov/Taxonomy/ taxonomyhome.html/index.cgi?chapter=extinct

EXPASY Biochemical Pathways

Finding out about the biochemical pathway

http://www.expasy.ch/cgi-bin/search-biochem-index

NCBI VecScreen

Removing vector sequence contamination and other artifacts in a DNA sequence

http://www.ncbi.nlm.nih.gov/VecScreen/ VecScreen.html

WebCutter

Restriction mapping for uncovering the enzymes that could cut a given DNA sequence

http://rna.lundberg.gu.se/cutter2/

NCBI ORF Finder

Viewing the different open reading frame of a DNA sequence

http://www.ncbi.nlm.nih.gov/projects/gorf/

ProtParam

Deducing the physico-chemical property of a protein

http://www.expasy.ch/tools/protparam.html

PFAM

Uncovering motif in amino acid sequence

www.sanger.ac.uk/software/pfam