APPLICATIONS OF BIOINFORMATICS
The various kinds of analysis which can be done using Bioinformatics tools are the following:
a) Processing raw information obtained from bench work done by researchers.
b) Tradition of genes using computer programmes like GENEMARK for prokaryotes and GENESCAN for eukaryotes.
c) Predicting protein sequences using computer programmes.
d) Identifying regulatory sequences such as enhancers and UAS using computer programme.
e) Deriving phylogenetic relationships amongst different organisms.
INFORMATION SOURCES AND MAJOR DATABASES
The National Centre of Biotechnology Information (NCBI) was created by the National Institute of Health, USA in 1988 to develop information systems in molecular biology. It provides Gen Bank nucleic acid sequence database, data retrieval systems and computational resources for the analysis of Gen Bank data. ENTREZ is NCBI’s search and retrieval system that provides users with integrated access to sequencing, mapping, taxonomy and structure data. BLAST (Basic Local Alignment Search Tool) is a program for sequence similarity searching and is also used in identifying genes and genetic features.
Classification of the resources available from NCBI
a) Database Retrieval tools like ENTREZ, TAXONOMY, BROWSER, LOCUS LINK. The taxonomy browser gives information about the taxonomic classification of various species. Locus link has information on the official gene names and other descriptive information about genes.
b) BLAST family of sequence similarity search programmes.
c) Gene level sequences which has several tools like Unigene, Homologene, RefSeq etc. Homologene is a database of orthologs and homologs for the human, mouse, rat, zebra fish and cow genes represented in Unigene and Locus link. Refseq is a database of mRNAs and proteins of human, mouse and rat which has helped in designing gene chips and describing the sequence features of the human genome.
d) Chromosomal sequences.
e) Genome analysis.
f) Analysis of gene expression patterns.
g) Molecular structure.
All these web based tools are available free.
ESTs stands for Expressed Sequence Tags. These comprise of partial cDNA clones i.e. cDNAs sequence from one end. It has its own special database called the dbEST. EST data can give information regarding the expression patterns by counting the Number of ESTs corresponding to each gene divided by the total number of ESTs.
GSTs stands for Genomic Sequence Tags. In Plasmodium falciparum the enzyme Mung Bean nuclease (Mnase) cuts between the genes. The digested DNA can be used to prepare genomic library. The sequences can be read from either ends as in ESTs.