An Over view of Bioinformatics

Bioinformatics: Application of it to the storage, retrieval and analysis of biological information, facilitated by the use of computer.

The central dogma of Bioinformatics Sequence-Structure-Function Evolution :In view-Invitro-Insilico The process of evolution has produced DNA sequences that encode proteins with very specific functions.

Good Bioinformatician
Biological Language Chemistry Computational principles

Components of Bio information

Sequence Analysis/Genomics Structural Biology/Proteomics Chemo informatics/Drug Designing Biocomputing

Database Management
Databases are created to store, retrieve and analyze the Biological data across the globe. Databases: Primary Databases: NCBI, EMBL, DDBJ Secondary Databases: PDB, Sequence DB, Structural DB, Motif DB, Genome DB, Proteome DB.

Accession no, g i-Gene id

NCBI www.ncbi.nlm.nih.gov/Gene bank EMBL www.ebi.ac.ac.uk/embl/ebi DDBJ www.ddbj.nig.ac.jp Unigene www.ncbi.nlm.nih.gov/unigene/tissue information SCD database www.staford.edu/Saccharomyces/yeast

NCBI TOOLS
ORF-Open reading frame(select largest exon) Map viewer- Select organism(gene name) Vec Screen- Unwanted, contaminated nucleotides) Electronic PCR- Primers, forward PCR, Reverse PCR Human genome resource- Compares only humans

 Bioedit (Offline tool) Primary analysis of protein: Nucleotide sequence, graphic representation, complementary sequence, reverse complementary, RNA sequence, transcription, restriction mapping BLAST The nucleotide sequence is generated in fasta format. Distribution of 158Blast hits on the query sequence has been is seen

Phylogenetic Analysis
Inthelastfewdecades,advancesinmolecular biology and the equipment available for research in this field have allowed the rapid sequencing of genomes of several species Computational Biology involves phylogenic trees to examine evolutionary relations

Tools:Offline Pdraw: Rooted tree. Unrooted tree, Radial tree Phylodraw :Root distance, Pair distance It is used to see root distance. It gives Unrooted tree, rooted tree and radial tree. In Phylogram the distance between related species is seen. In cladogram branching is seen.

 Clustal X :Multiple sequence alignment Online Clustal w : Multiple sequence alignment

 Primer 3 (On line) Submit nucleotide sequence . It gives primers.

Proteomics
Gen Scan (On line) Paste nucleotide sequence- It gives protein sequence (peptides) Gene Mark (Online)- Paste nucleotide sequence-It gives protein sequence(Viruses)

Protein Databases
Primary Structural database Swiss-Prot Secondary Structural databases and TrEMBL and PIR www.expasy.org Primary structural analysis Prot param Prot scale

Secondary structural analysis Tr EMBL, prosite ,Pfam Tools GOR,SOPMA Tertiary structural analysis PDB,SCOP,CATH

Visualization of protein
Tools RASMOL Cn3D Argus Lab HEX

Post Translational Modification

Signal P : peptide that binds to the protein which help to cross the nuclear membranecan delete the signal peptides. Sulfonators : Only thyrosine molecule can take sulfonate Net Acetyl : Acetylation of proteins Net O Glyc : Glycoprotein Net n Glyc : n Glycosylic bonds

Active site prediction

Heteroatom Cavity Q-site finder: Q site Finder gives the active sites for the protein molecule.

Energy Minimization
It is done for the stability of protein. The protein structure of the virus that has been stabilized will be used for drug design. Tools Spdbv, Argus Lab, Hex

Drug Databases
Drug Bank: We have drug database has Drug Bank from where we can find the suitable drug and go for further modification Ligand Info: Ligand Info system is based on the assumption that small molecules with similar structure have similar functional properties. The developed system enables a fast and sensitive index based search for similar compounds in large databases.

Tools used to design a drug

Chem draw tool can be used to draw the drug molecule accordingly. Hyperchem is used for proper geometric optimization. After the ligand is designed it has to go for QSAR Properties. Argus Lab is used for molecular modeling, graphics and drug designing

Conclusion
Using all these tools a novel drug for a foreign protein can be designed.

Drug Design
Tools: Free Hyperchem-Docking Argus Lab-Docking Licensed CACHE-Construction of molecule VEGA-Molecular Modeling