Sno

Database

Site

Use

Protein

Uniprot

http://www.uniprot.org/

Protein knowledgebase database  consists of two sections:

(A) Swiss-Prot: manually annotated and reviewed.

(B) TrEMBL: automatically annotated and is not reviewed.

Includes complete and reference proteome sets.

UniRef

http://www.uniprot.org/uniref/

Sequence clusters, used to speed up sequence similarity searches.

UniParc

http://www.uniprot.org/uniparc/

Sequence archive, used to keep track of sequences and their identifiers.

NCBI

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

Protein database collects sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

PRINTS

http://bioinf.man.ac.uk/dbbrowser/PRINTS/index.php

A collection of protein fingerprints (conserved motifs used to characterise a protein family)

PIR

http://pir.georgetown.edu/

Protein Information Resource (PIR), an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies

Pfam

http://pfam.xfam.org/

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)

Genes

Genebank

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

Text and similarity searching of the GenBank sequence database provided by the National Center for Biotechnology Information (NCBI).

Genedb

http://www.genedb.org/Homepage

GeneDB is a genome database for eukaryotic and prokaryotic pathogens

NCBI

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

Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

Structure

       1.

RCSB  (The Research Collaboratory for Structural Bioinformatics)

http://www.rcsb.org/pdb/home/home.do

The Protein Data Bank is a repository for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids.

      2.

CSD ( Cambridge Structural Database)

http://www.ccdc.cam.ac.uk/pages/Home.aspx

The repository of small molecule crystal structures

3.

ICSD ( Inorganic Crystal Structure Database)

http://icsd.ill.eu/icsd/index.php

ICSD is a database of inorganic crystal structure data, contains information on inorganic crystal structures published since 1913, including pure elements, minerals, metals, and intermetallic compounds (with atomic coordinates).

4.

BTPRED

(Beta-Turn Prediction Server)

http://www.biochem.ucl.ac.uk/bsm/btpred/index.html

BTPRED predicts the location and type of beta-turns in protein sequences. Predictions are made using a combination of artificial neural networks and simple filtering rules.

5.

CATH / Gene3D

http://www.cathdb.info/

CATH classifies protein structures (downloaded from the Protein Data Bank) and domains into superfamilies’ when there is sufficient evidence that they have diverged from a common ancestor.

6.

Swiss model repository

http://swissmodel.expasy.org/repository/

It is a repository for protein structure homology models

Phylogenetic  analysis

1.

PHYLIP ( PHYLogeny Inference Package)

http://bioweb2.pasteur.fr/

PHYLIP is a free package of programs for inferring phylogenies.

2.

Phylogeny.fr

http://www.phylogeny.fr/

Phylogeny.fr web server is dedicated to reconstructing and analyzing phylogenetic relationships between molecular sequences.

3.

moyble@pasteur

http://mobyle.pasteur.fr/cgi-bin/portal.py#welcome

Create workflows and save them for fast and easy reuse

Alignment

(A)

Global alignment

1.

CLUSTALw

http://www.genome.jp/tools/clustalw/

2.

Clustal omega

http://www.ebi.ac.uk/Tools/msa/clustalo/

Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments.

3.

Clustal w2

http://www.ebi.ac.uk/Tools/msa/clustalw2/

ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.

4.

Expasy

http://www.ch.embnet.org/software/ClustalW.html

5.

MAFT

http://www.ebi.ac.uk/Tools/msa/mafft/

Multiple alignment program for amino acid or nucleotide sequences

(B)

Local alignment

1.

blastp

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE

=BlastSearch&LINK_LOC=blasthome

Search protein database using a protein query

Algorithms used: blastp, psi-blast, phi-blast, delta-blast

2.

blastn

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE

=BlastSearch&LINK_LOC=blasthome

Search a nucleotide database using a nucleotide query

Algorithms used: blastn, megablast, discontiguous megablast

3.

blastx

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE

=BlastSearch&LINK_LOC=blasthome

Search protein database using a translated nucleotide query

4.

tblastn

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=&LINK_LOC

=blasttab&LAST_PAGE=blastx

Search translated nucleotide database using a protein query

5.

tbblastx

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch&BLAST_SPEC=&LINK_LOC

=blasttab&LAST_PAGE=tblastn

Search translated nucleotide database using a translated nucleotide query