FindingRetrievingSimilarityHomologyAlignment.pptVIP

Raw Genome Data: Finding Genes in GenBank: Entrez Web-based search engine for GenBank DNA and protein sequences as well as MEDLINE references Gene names, protein names, names of organisms or biological functions. Entrez is also a Database Pre-computed list of relationships between all of its data elements All nucleotide and protein sequences in GenBank (updated daily) along with all of the literature in MEDLINE and the 3-D protein structures in PDB (Protein Data Base) Internally Cross-linked DNA and protein sequences are linked to other similar sequences MEDLINE citations are linked to other citations that contain similar keywords 3-D structures are linked to similar structures Databases contain more than just DNA protein sequences Type in a Query term Enter your search words in the query box and hit “Go” or “Return/Enter” You can search for a text term in sequence annotations or in MEDLINE abstracts, and find all articles, DNA, and protein sequences that mention that term. Then from any article or sequence, you can move to related articles or related sequences. Miscellaneous These pre-computed relationships might include genes in the same multi-gene family, articles written about genes that have the same function, or other proteins that function in the same biochemical pathway This potential for horizontal movement through the linked databases makes Entrez really exciting; so you can think like a biologist, not a database programmer! A researcher can start with only a vague set of keywords or a sequence identified in the laboratory and rapidly access a set of relevant literature and a list of related database sequences. Database Search Strategies General search principles - not limited to sequence (or to biology). Use accession numbers whenever possible. Start with broad keywords and narrow the search using more specific terms. Try variants of spelling, numbers, etc. Search all relevant databases. Save your results locally! Refine the Query Often a se