Databases

INSDCInternational Nucleotide Sequence Database Collaboration

GenBank EMBL DDBJ

Sequence types:

Eukaryotic gene

Bacterial operon

Artificial Cloning vectors

Plasmid

Repeat element

Transfer RNA

GenBankNucleic Acids Research, 2008, 36, D25-D30

GenBankDoubled in size about every 18 months

80 billion nucleotide bases from more than 76 million individual

sequences

Sequence-based taxonomy

2,60,000 named species

1700 species are being added per month

12 % are human origin & 8% are human EST

The top species

Homo sapiens ------- 12.7 billion

Mus musculus ------- 8.3 billion

Rattus norvegicus ------- 5.8 billion

Bos taurus ------- 3.8 billion

Zea mays ------- 3.6 billion

GenBank Records and Divisions

GenBank records

Partitioned into “divisions”

Traditional BCT, VRL, PRI, ROD

Recent EST, GSS, HTG, HTC, ENV

WGS

Special TPA

WGS Accession numbers are issued to these sequences

eg., AAAA01072744

AAAA Project ID

01 Version number

072744 Contig number

TPA Third party annotation

1. Experimental

2. Inferential

Data submission

BankIt

Use BankIt if: you have one or a few sequence submissions you prefer to use a WWW-based submission tool your sequence annotation is not complicated you do not require sequence analysis tools to submit your sequence(s)

Sequin

Use Sequin if: you are submitting long or complex submissions you are submitting mutation, phylogenetic, population, environmental, or segmented sets you would like graphical viewing and editing options, including the alignment editor you would like network access to related analytical tools

EMBL

EMBLMaintained by EBI

Other databases of EBI

Swiss-Prot

TrEMBL

UniProt

InterPro

E-MSD

ArrayExpress

EMBLTaxonomic

Invertebrates, Organells, Bacteriophages, Plants, Prokaryotes, Rodents

Non-Taxonomic

HTG, HTC, GSS, WGS, EST

EMBL representationFor Genomic data Coding strand

cDNA data RNA sequence

tRNA Mature transcript

WebIn Data submission tool

DDBJ

DDBJEntry, format, abbreviation key same as GenBank

SAKURA Data submission tool

Secondary Nucleotide Sequence Databases

UniGene

Database of unique

gene clusters

STACK (Sequence Tag Alignment and Consensus Knowledgebase)

Ribosomal database

HIV sequence database

EPD (Eukaryotic Promoter Database)

REBASE

SwissProtCurated protein sequence database

High level of annotation

Description of the function

Domains structure

PTMs

Variants

TrEMBL

Consists of entries in SWISS-PROT-like format

PIR-PSDProtein Information resource- Protein Sequence Database

World’s first database of classified and funtionally annotated

protein sequences

Grew out of The Atlas of Protein Sequence and Structure

UniProtUniversal Protein Resource

Comprehensive resource for protein sequence and annotated

data

Sequence AlignmentsAlignments:

Pairwise

Multiple

Multiple Sequence Alignments provide information on,

Alignment itself

Consensus Sequences

Conserved residues

Conserved residue patterns

Sequence Profiles

Consensus Sequence DatabasesMultiple Alignment

↓

A single sequence in which each residue is the most common or consensus for the sequence family

↓

Consensus Sequence Database

Consensus Sequence Databases Disadvantage:

Much information from the sequences that do not contain the consensus residue is ignored, even though these hold information about allowed substitutions.

PROSITE Database of sequence patterns Associated with protein family membership. Developed using patterns that best fit particular protein

families and functions.

PROSITE

Serine Protease Family :- Pattern1:

[LIVM]-[ST]-A-[STAG]-H-C Pattern2:

[DNSTAGC]-[GSTAPIMVQH]-x(2)-G-[DE]-S-G-[GS]-[SAPHV]-[LIVMFYWH]-PA-[LIVMFYSTANQH]

PROSITEFeatures:

1.Much shorter than total sequence length

2.Provide information on acceptable substitution.

3.Provide information on shared biological functions.

PROSITEDisadvantage:

1. Lack of specificity.

2. They have no way of attaching

probabilities to the variation.

PRINTS and BLOCKS Contain multiply aligned ungapped segments.

BLOCKS- blocks

PRINTS - motifs

PRINTS and BLOCKS Advantages

1. Potentially more sensitive (more

distant relationships can be found)

2.More specific (fewer false positives

occur)

Specialized Sequence Database rRNA database tRNA database 5S rRNA database Promoter sequence database InBase, a database on inteins

OMIM Online Mendelian Inheritance in Man Comprehensive database of human genes and genetic

disorders. Has numerous links to databases like SWISS- PROT,

PubMed, Mutation databases, Mapviewer.

Structural Databases RCSB

1. PDB

2. NDB

Structural Databases PDBe of EBI

MMDB

Structures derived from the PDB, with value-added features

such as,

Explicit chemical graphs,

Links to literature,

Similar sequences,

Related 3D structures,

Information about chemicals

Structural DatabasesCATH

C- Class

A- Architecture

T- Topology

H- Homologous superfamily

SCOP

Structural Classification of Proteins

Higher Order Functions Databases KEGG (Kyoto Encyclopedia of Genes and Genomes)

Subsidiary Databases

Contains 16 main databases

Higher Order Functions Databases

DIP (Database of Interacting Proteins)

BIND (Biomolecular Interaction Network Database)

Literature Databases PubMed Web of Science BioMedNet

Data retrieval tools

Data retrieval toolsEntrez