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Biological databases
International nucleotide sequence
Database collaboration.
DDBJ (Japan)
EMBL
European Molecular
Biology Laboratory
http://www.ebi.ac.uk
PubMed,
GenBank
Nucleotides
(NCBI)
Proteins
http://www.ncbi.nlm.nih.gov
Genomes
Taxonomy
Structure
Domains
NCBI - GenBank
•
GenBank: All publicly available nucleotide and amino acid
sequences.
•
Data Source:
1.
2.
3.
•
Direct submission from scientists
Literature.
Genome Sequencing
DNA database divisions (examples)
1.
2.
3.
Organism division (Human, Bacteria, etc).
Molecule division (DNA, RNA, protein).
Sequence division (Genome, ESTs STSs).
sequence databases
An 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 NCBI
accession numbers
apply to a complete
sequence record
sequence identification numbers
apply to the individual sequences
within a record
GI number
assigned consecutively
by NCBI to each
sequence it processes
Version number
accession 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 format
See http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
GenBank
format
FASTA format
Example:
>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 format
entry
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 Database
http://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 database
http://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.
SRS
http://srs.ebi.ac.uk/
Choose
Library
Fill
Query form
Get
Results
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.
Gene
http://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
Refseq
http://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 division
Uses:
1.
2.
3.
Gene predication.
Expression level (only clues).
Alternative splicing.
Problems:
1.
2.
3.
Redundant database.
mistakes (single read-through).
Incomplete coverage of genes:
-
Only for Model eukaryotic organisms
Rare tissues
Low copy number of genes
UniGene
http://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…
Annotation Tracks
sequence Genome backbone: base position number
chromosome band
sts sites
gap locations
known genes
predicted genes
microarray/expression data
evolutionary conservation
SNPs
repeated regions
more…
Links out to
more data
Solution: Genome Browsers,
Or “map Viewers”
NCBI Map Viewer
http://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
General information
navigate
Specific information—
new features, current status, etc.
UCSC Material developed by
W.C. Lathe and M. Mangan,
[email protected]