Computer Storage of Sequences

1
Computer Storage of Sequences
(Chapter 2 of Bioinformatics Sequence and
Genome Analysis By David W. Mount)

• CSE730 Seminar on
• Information Retrieval of Biomedical Text and
  Data

2
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.

3
Nucleotide Sequence
Nomenclature Committee of the International Union of Biochemistry Nomenclature Committee of the International Union of Biochemistry Nomenclature Committee of the International Union of Biochemistry Nomenclature 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)
4
Protein Sequence
Code 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)
5
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.

6
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

7
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

8
Databases (continued)

• SwissProt
• The SwissProt protein sequence database at
  ISREC, Swiss Institute for Experimental Cancer
  Research.
• EMBL
• European Molecular Biology Laboratory (EMBL)
  Outstation at Hixton, England
• DDBJ
• DNA DataBank of Japan (DDBJ) at Mishima, Japan

9
Databases on Internet

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

10
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.

11
NCBI Integrated Databases

• Literature Databases
• Pubmed
• PubMed Central
• OMIM
• PROW
• BookShelf

12
NCBI Integrated Databases (continued)

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

13
NCBI Integrated Databases (continued)

• Entrez Databases
• Pubmed
• Protein Sequence Database
• Nucleotide Sequence Database
• Taxonomy
• OMIM

14
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.

15
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

16
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

17
NCBI Tools

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

18
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

19
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.

20
NCBI BLAST (continued)

• Access to BLAST service
• Web-BLAST
• Standalone BLAST
• Network BLAST
• BLAST URL API

21
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

22
NBRF PIR

• Protein Information Resource
• 3 Major Databases
• PSD (Protein Sequence Database)
• iProClass
• PIR-NREF
• (Nonredundant REFerence protein database)

23
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.

24
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/

25
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

26
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.

27
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.

28
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

29
Sequence Format Conversion

• READSEQ
• 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

30
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/

31
Thank You ?
Presented byHemal Patel Jeetal Shah