On line (DNA and amino acid) Sequence Information

Lecture 9

Introduction

• Annotation of genes• Basic bioinformatics Databases• NCBI home page• Query and return results• DNA sequence results page• Protein sequence results page

Bioinformatcs Databases• The Biological data, generated by various labs, is

submitted and stored in specific databases is : • The data is Nucleotide: DNA and mRNA (cDNA)

and Proteins sequences• The main “primary” nucleotide sequence

databases are:– United states: Genebank (NCBI) – Europe: Nucleotide sequence database (EMBL)– Japan: DNA databank of Japan.

• These databases also contain sequences related to: – Expressed sequence tags (ESTs) small (800 bp) of mRNA

and can be used to see what genes are expressed…

Protein Databases

• The main protein databases is:• Uniprot: (universal Protein resource)• Uniprot (KB) databases contains data from– SWISS-PROT (most up-to date information)– Trembl: (translation of coding sequences.)– PIR database

• Both the nucleotide and databases contain much more detail than sequences and the detail is referred to annotation.

Global Sequence 5

Annotation of sequences

• Once the gene sequence’s have been determined then the data must be annotated: (Klug 2010)– Identify regulatory regions – Other sequences of interest: exons/ introns, coding

sequences (cds), polyA signal– In protein annotation there are mRNA sequences– Other organisms where the DNA sequence/ AA

sequence is to found– Journals/Reference to where data came from.

Bioinformatics Database

• Bioinformatic Databases contain information for various biological data:

• To faciliate finding information there are a number of specific search engines:– NCBI has ENTREZ– EMBL has SRS

• Consider the following query:– What is the DNA and amino acid sequence for the

following gene: Human BTEB – more detail on the terms can be found by looking at a

sample record: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord

NCBI Entrez search page

Nucleic Record

Coding section of gene

The Exon intron structure is also available in graphic form

Protein records

Other databases databases

• The nucleotide (Genbank and EMBL) and protein (Uniprot) contain the “raw data” and are referred to as primary databases.

• More specific databases derive data from these and are referred to as secondary database; examples include protein family and sequence similarity databases such as PROSITE and PRINTS

• There are databases which contain information about specific organisms such as e. coli using Genome online database (GOLD)

Other databases

• Databases for specific types of sequences such as those associated with promoters and other regulatory elements.

• Others include structural databases from the Protein Data Bank

• On-line Mendelian inheritance of man (OMIM) which contains information on human genes and genetic disorders.

Bioinformatics Search Engines

• The Entrez (NCBI) search engine retrives information from NCBI databases and can be used to obtain other information including publications (Pubmed), 3D protein structures, online mendellian inheritance of Man…. A tutorial can be found at: – Entrez: Making use of its power:

• The EMBL uses ExPASy site which utilises the open source application: Sequence retrival system: a tutorial can be found at: – SRS tutotial: quick tour

Other important information sources• PUBMED: Literature research: journal articles/

conference proceedings/ books etc.– Search under many fields: keyword, author….– Returns: journal articles/abstracts– Two types: general/review.

• NCBI account: set up an NCBI account to manage previous searches….

• BTEB pubmed search found at:– http://www.ncbi.nlm.nih.gov/pubmed?term=BTEB&c

md=DetailsSearch

BTEB pubmed search result