Biological databases

International nucleotide sequence Database collaboration.

GenBank(NCBI)

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

EMBLEuropean Molecular Biology Laboratoryhttp://www.ebi.ac.uk

DDBJ (Japan)

PubMed, Nucleotides Proteins Genomes Taxonomy Structure Domains

NCBI - GenBank• GenBank: All publicly available nucleotide and amino acid

sequences.

• Data Source: 1. Direct submission from scientists

2. Literature.

3. Genome Sequencing

• DNA database divisions (examples)1. Organism division (Human, Bacteria, etc).

2. Molecule division (DNA, RNA, protein).

3. Sequence division (Genome, ESTs STSs).

sequence databasesAn optimal database should be:

Comprehensive, well annotated, easily searched & easy data retrieval, provide cross-references

The GenBank database:

As of April 2004, there are over 8,989,342,565 bases in GenBank.

Problems 1: huge databases Redundancy and inadequate sequences.

Problem 2: Submission by users Redundancy, Only the submitter can change it, not always up to date, partial annotation.

GenBank• HELP!!! http://www.ncbi.nlm.nih.gov/entrez/query/static/help/helpdoc.html

Unique Identifiers at NCBIaccession numbersapply to a complete

sequence record

sequence identification numbersapply to the individual sequences

within a record

GI numberassigned consecutively

by NCBI to each sequence it processes

Version numberaccession number followed

by a dot and a version number.

•The format of accession numbers varies, depending upon the source database:•GenBank/EMBL/DDBJ - One letter followed by five digits, e.g.:U12345 or two letters followed by six digits, e.g.:AY123456 •Swiss-Prot - All are six characters: [O,P,Q][0-9][A-Z,0-9][A-Z,0-9][A-Z,0-9][0-9] e.g.:P12345 and Q9JJS7 •RefSeq - Two letters, an underscore bar, and six digits, e.g.:NM_000492 (mRNA) NT_ (contig) NC (chromosome) NG (genomic region).

• If a sequence changes in any way, it receives a new GI number, and the version number is incremented by one.

GenBank formatSee http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html

GenBank format

FASTA formatExample:

>my_sequence_name

BTYKLJGJFKHVHFMGHF

KHGJFJFVKHGJHLNLNLJ

KJGKGKGKHLJH

• Easy to parse• Least informative• Default input format for sequence analysis

software (e.g., BLAST, CLASTALW).

Swiss-Prot (http://www.ebi.ac.uk/swissprot/)

• Core data: sequence, taxonomy and bibliographic reference.

• Annotation data: function, domain structure, post-translational modifications, protein

variants, etc.

– a curated protein sequence database

– provide a high level of annotation

– minimal level of redundancy

– high level of integration with other databases (cross references).

TrEMBL

• a computer-annotated supplement of Swiss-Prot that contains all the translations of EMBL

nucleotide sequence entries not yet integrated in Swiss-Prot.

ExPASy Proteomics Server http://www.expasy.org/

Swiss-Prot file formatentry

Flat-file original Swiss-Prot format

Search sequence databases

Two search methods– Text based searching– searches textual

information contained in header sections of database entries

– Sequence search– searches sequence information with sequence queries – next week!

Text based searching- Search for query words in specific fields.

- Choose your database and add limits.

- Examples: Entrez, SRS.

NCBI – Entrez (http://www.ncbi.nih.gov/Entrez/)• Entrez is the search tool for NCBI databases.• The search starts by choosing the relevant group of databases (Nucleotide,

Protein, etc).• Use field qualifiers, logical operators, and a “limits” form.• Boolean operator, AND, OR, NOT Group together by using ()Example:

cytochrome AND human cytochrome AND (human OR mouse)

• Always use upper case for operators.• If you don’t use any operator the query words are looked together!• Field qualifiers: Search in the specific field: Author, organism, journal …Example: • homo sapiens [organism] AND kinase AND nature [journal]

• Cytochrome b

• Cytochrome b AND human

• Cytochrome b AND human[organism]

• Cytochrome b AND human[organism] and limits.

Entrez Protein Databasehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

Includes SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.

Entrez Nucleotides databasehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide

• Includes GenBank, RefSeq, and PDB.

• As of April 2004, there are over 38,989,342,565 bases.

SRShttp://srs.ebi.ac.uk/

Choose Library

Fill Query form

GetResults

Gene-centric Databases

• Repository-type database:

- Many pieces of sequences related to a sequence

- Examples: GenBank/SwissProt

• Gene-centric database: - All the sequence information relevant to a given gene is made

accessible at once: Get the whole story at once!

- Provide easy access when the query is related to a gene or function.

- Examples: Gene, UniGene, RefSeq.

Genehttp://www.ncbi.nih.gov/entrez/query.fcgi?db=gene

• Gene provides a unified query environment for genes

• Query on names, symbols, accessions, publications, GO terms, chromosome numbers, E.C. numbers, and many other attributes associated with genes and the products they encode.

• Unique identifiers assigned to genes with known map positions.

• Supply key connections of map, sequence, expression, structure, function, citation, and homology data.

• Provide identifiers to UniGene, RefSeq, relevant GenBank entries,

OMIM and SNPs.

• Can be considered as the successor to LocusLink

Refseqhttp://www.ncbi.nlm.nih.gov/projects/RefSeq/

• non-redundancy  • distinct accession series • updates to reflect current knowledge of sequence data

and biology• ongoing curation by NCBI staff and collaborators,

with reviewed records indicated. • data validation and format consistency

ESTs divisionUses:

1. Gene predication.2. Expression level (only clues). 3. Alternative splicing.

Problems:

1. Redundant database.2. mistakes (single read-through).3. Incomplete coverage of genes:

- Only for Model eukaryotic organisms- Rare tissues- Low copy number of genes

UniGenehttp://www.ncbi.nlm.nih.gov/UniGene

• An automatically partitioning of GenBank sequences into a non-redundant set of gene-oriented clusters.

• Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.

• Focus on mRNA and EST information

Wouldn’t it be great if…

Genome backbone: base position numbersequenceA

nnot

atio

n T

rack

s

chromosome band

known genes

predicted genes

evolutionary conservation

SNPs

sts sites

gap locations

repeated regions

microarray/expression data

more…

Links out to more data

Solution: Genome Browsers,Or “map Viewers”

NCBI Map Viewerhttp://www.ncbi.nlm.nih.gov/Genomes/

Ensemble (http://www.ensembl.org/)

• Ensemble example: http://www.ensembl.org/Docs/linked_docs/human_eg_19_34.pdf

UCSC Home page ( genome.ucsc.edu )

navigate

navigateGeneral information

Specific information—new features, current status, etc.

UCSC Material developed byW.C. Lathe and M. Mangan,

info@openhelix.com