nucleic acid databases[1]

8/11/2019 Nucleic Acid Databases[1]

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Introduction to Bioinformatics

databases: Nucleic Acid

Databases

DineshGupta

ICGEB


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Biological databases: why?

Need for storing and communicating

large datasets has grown

Make biological data available to

scientists.

To make biological data available in

computer-readable form.


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Different classifications of

databases

Type of data

nucleotide sequences

protein sequences

proteins sequence patterns or motifs

macromolecular 3D structure

gene expression data

metabolic pathways


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Different classifications of databases.

Primary or derived databases

Primary databases: experimental results

directly into database

Secondary databases: results of analysis of

primary databases

Aggregate of many databases

Links to other data items Combination of data

Consolidation of data


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Technical design

Flat-files

Relational database (SQL)

Exchange/publication technologies (FTP,

HTML, CORBA, XML,...)


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Availability

Publicly available, no restrictions

Available, but with copyright

Accessible, but not downloadable

Academic, but not freely available

Proprietary, commercial; possibly free for

academics


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Where do I get DB of my interest ?


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http://www3.oup.co.uk/nar/database/c/
http://www3.oup.co.uk/nar/database/c/http://www3.oup.co.uk/nar/database/c/


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Nucleotide sequence databases

EMBL, GenBank, and DDBJ are the three

primary nucleotide sequence

databases

EMBL www.ebi.ac.uk/embl/

GenBank

www.ncbi.nlm.nih.gov/Genbank/

DDBJ www.ddbj.nig.ac.jp
http://www.ebi.ac.uk/embl/http://www.ncbi.nlm.nih.gov/Genbank/http://www.ddbj.nig.ac.jp/http://www.ddbj.nig.ac.jp/http://www.ncbi.nlm.nih.gov/Genbank/http://www.ebi.ac.uk/embl/


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Genbank

An annotated collection of all publiclyavailable nucleotide and proteins

Set up in 1979 at the LANL (Los Alamos).

Maintained since 1992 NCBI (Bethesda).

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


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EMBL Nucleotide Sequence

Database An annotated collection of all publicly available

nucleotide and protein sequences

Created in 1980 at the European Molecular

Biology Laboratoryin Heidelberg.

Maintained since 1994 by EBI- Cambridge.

http://www.ebi.ac.uk/embl.html
http://www.ebi.ac.uk/embl.htmlhttp://www.ebi.ac.uk/embl.html


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http://www3.ebi.ac.uk/Services/DBStats/
http://www3.ebi.ac.uk/Services/DBStats/http://www3.ebi.ac.uk/Services/DBStats/http://www3.ebi.ac.uk/Services/DBStats/http://www3.ebi.ac.uk/Services/DBStats/


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DDBJDNA Data Bank of Japan

An annotated collection of all publicly availablenucleotide and protein sequences

Started, 1984 at the National Institute ofGenetics(NIG) in Mishima.

Still maintained in this institute a team led by

Takashi Gojobori.

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


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Other NCBI nucleic acids DBs

EST database:A collection of expressed sequence tags, or short, single-pass sequencereads from mRNA (cDNA).

GSS database: A database of genome survey sequences, or short, single-pass genomicsequences.

HomoloGene:A gene homology tool that compares nucleotide sequences between pairs oforganisms in order to identify putative orthologs.

HTG database:A collection of high-throughput genome sequences from large-scalegenome sequencing centers, including unfinished and finished sequences.

SNPs database:A central repository for both single-base nucleotide substitutions andshort deletion and insertion polymorphisms.

RefSeq:A database of non-redundant reference sequences standards, including genomicDNA contigs, mRNAs, and proteins for known genes. Multiple collaborations, both withinNCBI and with external groups, supports data-gathering efforts.

STS database:A database of sequence tagged sites, or short sequences that areoperationally unique in the genome.

UniSTS:A unified, non-redundant view of sequence tagged sites (STSs).

UniGene:A collection of ESTs and full-length mRNA sequences organized into clusters,each representing a unique known or putative human gene annotated with mapping andexpression information and cross-references to other sources.
http://www.ncbi.nlm.nih.gov/dbEST/index.htmlhttp://www.ncbi.nlm.nih.gov/dbGSS/index.htmlhttp://www.ncbi.nlm.nih.gov/HomoloGene/http://www.ncbi.nlm.nih.gov/HTGS/http://www.ncbi.nlm.nih.gov/SNP/http://www.ncbi.nlm.nih.gov/RefSeq/http://www.ncbi.nlm.nih.gov/dbSTS/index.htmlhttp://www.ncbi.nlm.nih.gov/genome/sts/http://www.ncbi.nlm.nih.gov/UniGene/http://www.ncbi.nlm.nih.gov/UniGene/http://www.ncbi.nlm.nih.gov/genome/sts/http://www.ncbi.nlm.nih.gov/dbSTS/index.htmlhttp://www.ncbi.nlm.nih.gov/RefSeq/http://www.ncbi.nlm.nih.gov/SNP/http://www.ncbi.nlm.nih.gov/HTGS/http://www.ncbi.nlm.nih.gov/HomoloGene/http://www.ncbi.nlm.nih.gov/dbGSS/index.htmlhttp://www.ncbi.nlm.nih.gov/dbEST/index.html


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Sequence submission

Data mainly direct submissions from theauthors.

Submissions through the Internet:

Web forms. Email.

Sequences shared/exchanged between

the 3 centers on a daily basis: The sequence content of the banks is

identical.


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Derived databases

CUTG Codon usage tabulated from GenBank

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

Genetic Codes Deviations from the standard genetic code in various

organisms and organelles

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c

TIGR Gene Indices Organism-specific databases of EST and gene

sequences http://www.tigr.org/tdb/tgi.shtml

UniGene Unified clusters of ESTs and full-length mRNA sequences

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

ASAP Alternative spliced isoformshttp://www.bioinformatics.ucla.edu/ASAP

Intronerator Introns and alternative splicing in C.elegans and

C.briggsae http://www.cse.ucsc.edu/~kent/intronerator/
http://www.kazusa.or.jp/codon/http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=chttp://www.tigr.org/tdb/tgi.shtmlhttp://www.ncbi.nlm.nih.gov/UniGene/http://www.bioinformatics.ucla.edu/ASAPhttp://www.cse.ucsc.edu/~kent/intronerator/http://www.cse.ucsc.edu/~kent/intronerator/http://www.bioinformatics.ucla.edu/ASAPhttp://www.ncbi.nlm.nih.gov/UniGene/http://www.tigr.org/tdb/tgi.shtmlhttp://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=chttp://www.kazusa.or.jp/codon/


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Nucleic acid structure

databases NDB Nucleic acid-containing structures

http://ndbserver.rutgers.edu/

NTDB Thermodynamic data for nucleic acidshttp://ntdb.chem.cuhk.edu.hk/

RNABase RNA-containing structures from PDB andNDB http://www.rnabase.org/

SCOR Structural classification of RNA: RNA motifs bystructure, function and tertiary interactions

http://scor.lbl.gov/
http://ndbserver.rutgers.edu/http://ntdb.chem.cuhk.edu.hk/http://www.rnabase.org/http://scor.lbl.gov/http://scor.lbl.gov/http://www.rnabase.org/http://ntdb.chem.cuhk.edu.hk/http://ndbserver.rutgers.edu/


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Database searching tips

Look for links to Helpor Examples

Try Booleansearches

Be careful with UK/US spellingdifferences leukaemia vs leukemia

haemoglobin vs hemoglobin

colour vs color


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Exercises Study the statistics of the three primary nucleic acid

databases: Are they matching ?

Look for a gene of your interest in the three primarynucleic acid databases: compare the information given ineach one of them.

Read NAR DB paper and NAR DB index site: search fordifferent nucleic acid databases based on differentsearch terms.

Self study:

http://www3.oup.co.uk/nar/database/c/ Download NAR database paper (NARDB2004) from:ftp://cbag.sc.mahidol.ac.th/pub/Course_Materials/dinesh
http://www3.oup.co.uk/nar/database/c/http://www3.oup.co.uk/nar/database/c/

nucleic acid databases[1]

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