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
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 A Alanine N Asparagine B 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 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
SwissProt
EMBL
DDBJ

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.
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

31. Thank You 
Presented by: Hemal Patel & Jeetal Shah