Computer Storage of Sequences

CSE730: Seminar on “Information Retrieval of Biomedical

Text and Data”

(Chapter 2 of Bioinformatics: Sequence and Genome Analysis

By David W. Mount)

Outline

Storing DNA/Protein sequences into computer files or databases.

Related information placed in the database along with the sequence in a number of sequence data formats.

Online public access Databases for sequence retrieval.

Nucleotide SequenceNomenclature Committee of the International Union of Biochemistry

Code Nucleic Acid(s) Code Nucleic Acid(s)

A Adenine M A or C (amino)

C Cytosine R A or G (purine)

G Guanine W A or T (weak)

T Thymine S C or G (strong)

U Uracil Y C or T (pyrimidine)

K G or T (keto)

V A or C or G

H A or C or T

D A or G or T

B C or G or T

N A or G or C or T (any)

Protein SequenceCode Amino acid Code Amino acid

A Alanine N Asparagine

B Asparagine P Proline

C Cysteine Q Glutamine

D Aspartic acid R Arginine

E Glutamic acid S Serine

F Phenylalanine T Threonine

G Glycine V Valine

H Histidine W Tryptophan

I Isoleucine X Unknown

K Lysine Y Tyrosine

L Leucine Z Glutamine

M Methionine

Adapted from IUPAC-IUB (1969,1972, 1983)

Sequence Formats

Sequence is stored as ASCII text (i.e. sequence of A,G,C,T…) along with annotations.

Different sequence formats recognized by different sequence analyzer programs.

Sequence Format includes accessory information, gene names, source organism, investigator name, references, and the actual sequence.

Sequence Formats (continued)

FASTA GenBank Flat File format PIR/CODATA format EMBL sequence entry format Intelligenetics sequence entry format GCG (Genetics Computer Group) sequence

entry format. ASN.1 XML

Databases

NCBI

GenBank at the National Center of Biotechnology Information (NCBI), National Library of Medicine, Washington, DC

NBRF

Protein Information Resource (PIR) database at the National Biomedical Research Foundation in Washington, DC

Databases (continued)

SwissProtThe SwissProt protein sequence database at ISREC, Swiss Institute for Experimental Cancer Research.

EMBLEuropean Molecular Biology Laboratory (EMBL) Outstation at Hixton, England

DDBJDNA DataBank of Japan (DDBJ) at Mishima, Japan

Databases on Internet

NCBI http://www.ncbi.nlm.nih.govPIR

http://www-nbrf.georgetown.edu/pirwww

SwissProt http://www.expasy.ch/cgi-bin/sprot-search-de

EMBL http://www.ebi.ac.uk/embl/index.htmlDDBJ http://www.ddbj.nig.ac.jp/

NCBI

National resource for molecular biology information.

Maintains comprehensive databases for variety of Biotech related information.

Develops and manages access to a range of databases and softwares for scientific and medical communities.

NCBI : Integrated Databases

Literature Databases Pubmed PubMed Central OMIM PROW BookShelf

NCBI : Integrated Databases (continued)

Nucleotide Databases GenBank EST Database GSS Database SNPs Database RefSeq STS Database

NCBI : Integrated Databases (continued)

Entrez Databases Pubmed Protein Sequence Database Nucleotide Sequence Database Taxonomy OMIM

GenBank

GenBank is the NIH genetic sequence database.

Annotated collection of all publicly available DNA sequences.

GenBank is a part of an international collaboration of sequence databases along with EMBL and DDBJ.

GenBank DNA Sequence Format

DNA sequence in GenBank is formatted into distinct attributes as following

Locus: locus name, sequence length, division, date

Definition: description of entry

Accession: unique accession number

Version: version of sequence

Keywords: keywords for cross referencing

GenBank DNA Sequence Format(continued)

Source: source organism of DNA

Organism: description of organism References: authors, title, journal, Medline, etc

Features: information about sequence

Base count: number of bases in sequence

Origin: sequence data begin following origin.

Genebank sample

NCBI : Tools

Tools for Data Retrieval and submission Text Term Searching Sequence Similarity Searching Taxonomy Searching Sequence Submission

NCBI : ENTREZ

Entrez is a search and retrieval system that integrates information from databases at NCBI.

These databases include nucleotide sequences, protein sequences, macromolecular structures, whole genomes, and MEDLINE, PubMed. Etc.

Entrez

NCBI : BLAST

BLAST: Basic Local Alignment Search Tool It is a set of similarity search programs designed

to explore available sequence databases. It uses a heuristic algorithm which is able to

detect relationships among sequences which share only isolated regions of similarity

Q-BLAST: It is a queuing system to BLAST that allows users to retrieve results at their convenience and format their results.

NCBI : BLAST (continued)

Access to BLAST serviceWeb-BLASTStandalone BLASTNetwork BLASTBLAST URL API

NCBI : BLAST (continued)

BLAST Programs Blastp : Compares amino acid sequence against

protein sequence Database Blastn : Compares nucleotide sequence against

nucleotide sequence Database Blastx :Compares nucleotide query sequence against

protein sequence Database Tblastn : Compares protein query sequence against

nucleotide sequence Database

BLAST

NBRF :PIR

Protein Information Resource

3 Major Databases:PSD (Protein Sequence Database)iProClassPIR-NREF

(Nonredundant REFerence protein database)

PIR: PSD

The PIR, in collaboration with MIPS and JIPID, produces and distributes the PIR-International Protein Sequence Database (PSD) .

Comprehensive and expertly annotated protein sequence database.

The primary sources of PSD data are sequences from GenBank/EMBL/DDBJ translations, published literature, and direct submission to PIR-International.

PIR: PSD (continued)

The PIR-PSD data is available in XML format and NBRF, PIR/CODATA formats. The sequence file is available in FASTA format.

Also available at PIR UNIX FTP server. Address: ftp://ftp.pir.georgetown.edu/pir_databases/psd/

CODATA format

CODATA format has approximately the same information as a GenBank or EMBL sequence file, but is slightly differently formatted and has different field names.

Also called PIR format, used by NBRF.

CODATA Sample

PIR: iProClass

The iProClass database provides comprehensive descriptions of all proteins and serves as a framework for data integration in a distributed networking environment.

Very user-friendly description.

PIR: NREF (Non-redundant REFerence protein database) Comprehensive: Containing all sequences from PIR-PSD, Swiss-

Prot, TrEMBL, RefSeq, GenPept, and updated bi-weekly.

Non-Redundant: Clustered by sequence identity and taxonomy at the species level.

Source Attribution: Containing protein IDs and names from associated databases (with hypertext links), in addition to protein sequence, taxonomy, and bibliography.

The current version (July 2002) consists of more than 809,000 non-redundant PIR-PSD, SwissProt and TrEMBL proteins organized with more than 36,200 PIR superfamilies, 145,340 families, and links to over 50 molecular biology databases.

Swiss-Prot

Swiss-Prot is a protein knowledgebase established in 1986.

Maintained collaboratively, by the Department of Medical Biochemistry of the University of Geneva (now the Swiss Institute of Bioinformatics) and the EMBL Data Library.

Swiss-Prot Sequence Entry Example

Sequence Format ConversionREADSEQ: Sequence Format Conversion program.http://bimas.dcrt.nih.gov/molbio/readseq/

Can convert to/from: ASN.1 FASTA CODATA GCG EMBL format GenBank format and many other formats

References

http://www.ncbi.nlm.nih.gov http://www-nbrf.georgetown.edu/pirwww http://www.expasy.ch/cgi-bin/sprot-search-de http://www.ebi.ac.uk/embl/index.html http://www.ddbj.nig.ac.jp/

Thank You

Presented by:Hemal Patel &

Jeetal Shah