bioinformatics resources

Bioinformatics : 

Bioinformatics Resources and databases

What is bioinformatics? : 

What is bioinformatics? Bioinformatics or computational biology is the use of techniques from applied mathematics, informatics, statistics, and computer science to solve biological problems.

Examples of Bioinformatics : 

Examples of Bioinformatics Database interfaces Genbank/EMBL/DDBJ, Medline, SwissProt, PDB, … Sequence alignment BLAST, FASTA Multiple sequence alignment Clustal, MultAlin, DiAlign Gene finding Genscan, GenomeScan, GeneMark, GRAIL Protein Domain analysis and identification pfam, BLOCKS, ProDom, Pattern Identification/Characterization Gibbs Sampler, AlignACE, MEME Protein Folding prediction PredictProtein, SwissModeler

Major websites for bioinformatics analysis : 

Major websites for bioinformatics analysis NCBI (The National Center for Biotechnology Information; http://www.ncbi.nlm.nih.gov/ EBI (The European Bioinformatics Institute) http://www.ebi.ac.uk/ The Canadian Bioinformatics Resource http://www.cbr.nrc.ca/ SwissProt/ExPASy (Swiss Bioinformatics Resource) http://expasy.cbr.nrc.ca/sprot/ PDB (The Protein Databank) http://www.rcsb.org/PDB/

A few more resources to be aware of : 

A few more resources to be aware of Human Genome Working Draft http://genome.ucsc.edu/ TIGR (The Institute for Genomics Research) http://www.tigr.org/ Celera http://www.celera.com/ (Model) Organism specific information: Yeast: http://genome-www.stanford.edu/Saccharomyces/ Arabidopis: http://www.tair.org/ Mouse: http://www.jax.org/ Fruitfly: http://www.fruitfly.org/ Nematode: http://www.wormbase.org/ Nucleic Acids Research Database Issue http://nar.oupjournals.org/ (First issue every year)

BLAST : 

BLAST The different versions of BLAST

Databases : 

Databases Sequence database: Nucleotide Databases: RefSeq: Reference Sequence, EMBL: European Molecular Biology Laboratory, Genbank, DDBJ: DNA Data Bank of Japan Protein Databases:SwissProt: Swiss Protein, TrEMBL: Translated EMBL Entry names are often the name of the gene followed by the species. Accession numbers are of the following format: [O,P,Q] [0-9] [A-Z, 0-9] [A-Z, 0-9] [A-Z, 0-9] [0-9], e.g. P26367 (PAX6_HUMAN)

How to search a sequence in a database : 

How to search a sequence in a database Text Search: Use text with a boolean operator BRCA1 & BRCA2 – searches for BRCA1 AND BRCA2 BRCA1 | BRCA2 – searches for one gene OR the other BRCA1 ! BRCA2 – searches for BRCA1 BUT NOT BRCA2

Searching the databases with a “search engine”: : 

Searching the databases with a “search engine”:

Structural Databases : 

Structural Databases Tertiary protein structure prediction is possibly the Holy Grail of bioinformatics. PDB: Protein DataBank, New Jersey, USA http://www.rcsb.org/ EMSD: EBI Macromolecular Structure Database http://www.ebi.ac.uk/msd/index.html Management and distribution of data on macromolecular structures in close collaboration with the PDB. This houses a collection of 3D coordinates of each atom in a protein, allowing the structure to be displayed by viewing software. Protein structures are submitted by individual researchers and have been determined by x-ray diffraction, or NMR.