(a) Nucleotide Databases

These are the sequence databases which provide the nucleotide sequence of various organisms. There are mainly three main nucleotide sequence databases which are as following:

Database

Description

Url

National Center for Biotechnology Information (GenBank) 

It is the one of the major database which provides with DNA sequence data of various organisms in the form of Gen

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

EMBL Nucleotide Sequence Database 

EMBL Nucleotide Sequence Database maintains, organizes and distributes nucleotide sequence obtained from various sources.

http://www.ebi.ac.uk

DNA Data Bank of Japan(DDBJ)

DDBJ collects , annotates and distributes the nucleotide sequence data.

http://www.ddbj.nig.ac.jp

Apart from these others are as following:

Database

Description

Url

UCSC Genome Browser

University of California, Santa Cruz (UCSC) Genome Browser is an open integrated source for genomic sequence data from various varieties of vertebrates and invertebrate species

http://genome.ucsc.edu/

AsDb (Aberrant Splicing db)

It is a publically accessible portal which gives the information on information about alternatively spliced genes, their products and expression patterns.

http://www.hgc.jp/~knakai/asdb.html

Codon Usage Db

Codon Usage database is a non-redundant database which provides the information of the coding region of the genomes of various organisms

http://www.kazusa.or.jp/codon/

dbEST

It is the accumulation and analysis of Expressed Sequence Tags

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

dbSTS

It is the collection of various of Sequence tagged sites

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

Ensembl

Ensemble provides genomic databases for vertebrates and other eukaryotic species.

http://www.ensembl.org/index.html

SRS

It is a database which maintains nucleotide sequence of various organisms.

http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+srsq2+-noSession

 

 (b) Protein Sequence Databases

Protein sequence databases provide a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Some of the important protein sequence databases are as following:

Database

Description

Url

Uni-Prot:

United Protein Database

Uni-Prot database combines the information of the major international databases, European Bioinformatics Institute (EBI), Protein Information Resource (PIR) and Swiss Institute of Bioinformatics (SIB). It provides the scientific community with resources for protein sequences and functional information.

http://www.uniprot.org/

PIR

(Protein Information Resource)

The Protein Information Resource (PIR) is a bioinformatics portal which helps in scientific study by providing protein sequences and other details related to protein of query.

http://pir.georgetown.edu/

NCBI Protein resources

The NCBI Protein database is a collection of protein sequences from several sources, such as from SwissProt, PIR, PRF, and PDB and also by translations from annotated coding regions in GenBank, RefSeq and TPA

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

HPRD

The Human Protein Reference Database is a centralized platform to visually depict and integrate infor- mation pertaining to domain archi- tecture, post-translational modi- fications, interaction networks and disease association for each protein in the human proteome.

http://www.hprd.org/

Swiss Human Plasma Protein dataset

The Swiss Human Plasma Protein dataset provides biologists and biomedical researchers with a new gateway for exploring proteins from the human proteome with peptide-level evidence found in plasma.

http://www.expasy.org/

PIRSF

The PIRSF provides comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.

http://pir.georgetown.edu/

Many databases provide the details of proteins family and of which are as following:

Database

Description

Url

PROSITE 

PROSITE is a database of protein families and domains. It is based on the observation that a huge number of different proteins can be grouped on the basis of similarities in their sequences, into a limited number of families. Proteins domains belonging to a particular family generally share functional attributes and are derived from a common ancestor.

http://www.expasy.org/prosite

BLOCKS

The Blocks Database include multiple alignments of conserved regions in protein families. This database also helps in finding ligand binding regions, catalytic domains and transmembranal domains.

http://blocks.fhcrc.org

InterPro

InterPro hgive the classified sequences of protein at superfamily, family and subfamily levels and also predict the occurrence of functional domains, repeats and important sites.

http://www.ebi.ac.uk/interpro/

Pfam

The Pfam database is a large collection of protein families, each represented by multiple sequence alignmentsandhidden Markov models (HMMs). It also provides the details of the various domain regions in the particular protein.

http://pfam.sanger.ac.uk

TIGRFAMS

TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional identification of proteins by sequence homology.

http://www.jcvi.org/cms/research/projects/tigrfams/overview

STRING

It provides the protein sequence data , protein network data and protein interaction data.

http://string-db.org/

PANTHER

(Protein ANalysis  THrough Evolutionary Relationships)

The PANTHER is a unique resource that classifies protein on the basis of its function. It also classifies genes on the basis of their functrion.

http://www.pantherdb.org/

MEROPS Database 

he MEROPS database is a collection of peptidases which classifies the peptides on the basis of homology and and the peptides with similar functions.

http://merops.sanger.ac.uk/

SMART

( Simple Modular Architecture
Research Tool )

This database provides the proteomic as well as the genomic details of various organisms.

http://smart.embl-heidelberg.de/

ProDom 

ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences.

http://prodom.prabi.fr/prodom/current/html/home.php

PRIDE

( PRoteomics IDEntifications)

The PRIDE database is a centrealized public data repository for proteomics data. It has been developed to provide the proteomics community with a public repository for protein and the peptides

http://www.ebi.ac.uk/pride/

PeptideAtlas 

PeptideAtlas is a multi-organism database of peptides which are identified in a large set of tandem mass spectrometry proteomics experiments. It provides with data from human, mouse, yeast, and several other organisms

http://www.peptideatlas.org/

MIAPEGelDB

MIAPEGelDB is a web-based s public repository for MIAPE gel electrophoresis data.

http://miapegeldb.expasy.org/

World-2DPAGE Repository (All)

This database is the collection of the 2D PAGE experimental data.

http://world-2dpage.expasy.org/repository/

PIRSF 

The PIRSF provides comp- rehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.

http://pir.georgetown.edu/pirsf/

MIPS

(Munich Information  Center for Protein Sequences )

MIPS is a protein database which provides the sequence of various proteins.

http://www.helmholtz-muenchen.de/en/ibis

 

(c) RNA Sequence Databases

RNA Sequence Databases provides sequence of various Ribonucleic acids like miRNA, snRNA, mRNA, etc. The list of various databases is as following:

Database

Description

Url

RNA mod db

The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleo- sides from RNA

http://mods.rna.albany.edu/

smiRNAdb

smiRNAdb is a resource of miRNA pro?les determined by sequencing from hundreds of Homo sapiens , Mus musculus and Rattus norvegicus samples.

http://swik.net/lesstif/del.icio.us+tag-motif/smiRNAdb+--+Home+page/%20c13rd

tmRNA  

The tmRDB is a collection of the structures and functions of the tmRNAs

http://www.ag.auburn.edu/mirror/tmRDB/AbouttmRDB.html

Rfam 

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).

http://rfam.sanger.ac.uk/

miRBase 

The miRBase database is a of published miRNA sequences and annotation

http://www.mirbase.org/

5S rRNA

This database provides the information on nucleotide sequences of 5S rRNAs and their genes.

http://rose.man.poznan.pl/5SData/

ssu rRNA

This database contains the sequences and structures of ssu ribosomal subunit RNA

http://bioinformatics.psb.ugent.be/webtools/rRNA/ssu/

Isu rRNA

This database contains the sequences and structures of  lsu ribosomal subunit RNA

http://bioinformatics.psb.ugent.be/webtools/rRNA/lsu

 

Mamit-tRNA 

Mamit-tRNA is a compilation of mammalian mitochondrial tRNA genes.

http://mamit-trna.u-strasbg.fr/Summary.asp

fRNAdb

This database is a platform for mining or annotating functional RNA candidates from non-coding RNA sequences

http://omictools.com/frnadb-tool