Learn about Bioinformatic Databases

Bioinformatics databases are electronic stores of biological data.  Few examples of such  databases are as follows:

•  Nucleotide Sequence Databases: GenBank EMBL  DDBJ  
  • Updated and maintained on a daily basis
  • EMBL and DDBJ entries are also submitted  in GenBank
  • You can see a sample GenBank file, a more detailed explanation of the GenBank format, and definitions of the items in the GenBank Features Table can be seen at the original Via GenBank site
  • One  can submit Sequence data to GenBank using the program Sequin
  • To Search GenBank Web Add is http://www.ncbi.nlm.nih.gov

  Protein Sequence Databases: 

  SwissProt          PIR   PDB

   

  Database of Expressed Sequence Tags: dbEST

  • contains partial nucleotide sequences (generally single sequencing runs from both ends of the insert) of randomly picked cDNAs from different tissue libraries; EST entries are submitted from a wide variety of organisms and many represent novel genes

Gene Analysis Tools

ORF Finder

Open Reading Frame (ORF) Finder tool identifies all possible ORFs in a DNA sequence by locating the standard and alternative stop codons in all six reading frames of the corresponding translated amino acid sequence.  The ORFs are represented as shaded boxes. By clicking on a shaded box, the amino acid sequence of that ORF is displayed. The deduced amino acid sequences can then be automatically used to BLAST against GenBank sequences.
 

OMIM

Online Mendelian Inheritance in Man (OMIM) is a database containing information about human genes and genetic disorders which have been mapped onto the human genome. Typical OMIM entries contain a summary of each disease including clinical manifestations, genetic mapping information, a large list of related references, and a direct link to the DNA sequence in GenBank if the disease gene has been cloned. OMIM also contains mapping information on genes which have not yet been associated with disease. The database can be searched using several types of queries, and one can look for diseases and genes found within a specific map locus, or diseases which share common clinical symptoms.
   

Cancer Genome Anatomy Project (CGAP)

The Cancer Genome Anatomy Project (CGAP) aims to decipher the molecular anatomy of cancer cells.  CGAP develops profiles of cancer cells by comparing gene expression in normal, pre cancerous, and malignant cells from a wide variety of tissues.
 

VAST

VAST search is a structure-structure similarity search service.  It compares 3D coordinates of a newly determined protein structure to those in the MMDB/PDB database. VAST Search computes a list of  similar structures that can be browsed interactively, using molecular graphics to view super impositions and alignments.
 

UniGene

UniGene clusters repeated EST entries which represent the same gene. The majority of these clusters have been mapped onto the human genome by the International RH (radiation hybrid) Mapping Consortium. This database is also valuable for researchers looking for tissue-specific cDNAs because UniGene can list clusters containing ESTs found in only one tissue library.
 

VecScreen

VecScreen is a tool for identifying segments of a nucleic acid sequence that may be of vector, linker or adapter origin prior to sequence analysis or submission.  VecScreen was developed to combat the problem of vector contamination in public sequence databases.
 

Electronic PCR

The Electronic PCR feature allows you to search your DNA sequence for the presence of sequence tagged sites (STS), which have been used as landmarks in various types of genomic maps. The default is to search all STSs, but searches may be restricted to one organism by selecting it from the list below the input box. You may either enter sequences (in FASTA format) or enter GenBank accession numbers into the text box.
 

Copyright ©2001 eBioinfogen Innovatives. All Rights Reserved
editor@ebioinfogen.com