Introduction to Bioinformatics

databases: Nucleic Acid

Databases

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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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 Different classifications of databases….

• Technical design
– Flat-files
– Relational database (SQL)
– Exchange/publication technologies (FTP,
HTML, CORBA, XML,...)

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 Different classifications of databases….

• 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/

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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

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 Genbank
• An annotated collection of all publicly
available nucleotide and proteins

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

• Maintained since 1992 NCBI (Bethesda).

• 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 Laboratory in Heidelberg.

• Maintained since 1994 by EBI- Cambridge.

• http://www.ebi.ac.uk/embl.html
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 http://www3.ebi.ac.uk/Services/DBStats/

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DDBJ–DNA Data Bank of Japan
• An annotated collection of all publicly available
nucleotide and protein sequences

• Started, 1984 at the National Institute of

Genetics (NIG) in Mishima.

• Still maintained in this institute a team led by

Takashi Gojobori.

• 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 sequence
reads from mRNA (cDNA).
• GSS database: A database of genome survey sequences, or short, single-pass genomic
sequences.
• HomoloGene: A gene homology tool that compares nucleotide sequences between pairs of
organisms in order to identify putative orthologs.
• HTG database: A collection of high-throughput genome sequences from large-scale
genome sequencing centers, including unfinished and finished sequences.
• SNPs database: A central repository for both single-base nucleotide substitutions and
short deletion and insertion polymorphisms.
• RefSeq: A database of non-redundant reference sequences standards, including genomic
DNA contigs, mRNAs, and proteins for known genes. Multiple collaborations, both within
NCBI and with external groups, supports data-gathering efforts.
• STS database: A database of sequence tagged sites, or short sequences that are
operationally 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 and
expression information and cross-references to other sources.

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 Sequence submission
• Data mainly direct submissions from the
authors.
• 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 isoforms
http://www.bioinformatics.ucla.edu/ASAP
• Intronerator Introns and alternative splicing in C.elegans and
C.briggsae http://www.cse.ucsc.edu/~kent/intronerator/

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 Nucleic acid structure
databases
• NDB Nucleic acid-containing structures
http://ndbserver.rutgers.edu/

• NTDB Thermodynamic data for nucleic acids

http://ntdb.chem.cuhk.edu.hk/

• RNABase RNA-containing structures from PDB and NDB

http://www.rnabase.org/

• SCOR Structural classification of RNA: RNA motifs by

structure, function and tertiary interactions
• http://scor.lbl.gov/

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 Database searching tips
• Look for links to Help or Examples
• Try Boolean searches
• Be careful with UK/US spelling differences
– 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 primary
nucleic acid databases: compare the information given in
each one of them.
• Read NAR DB paper and NAR DB index site: search for
different nucleic acid databases based on different
search 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

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