Bioinformatics Resources and Tools on the Web A Primer.ppt

Bioinformatics Resources and Tools on the Web: A Primer Joel H. Graber Center for Advanced Biotechnology Boston University Outline Introduction: What is bioinformatics? The basics The five sites that all biologists should know Some examples Using the tools in a somewhat less-than-na?ve manner Questions/comments are welcome at all points Much of this material comes from the Boston University course: BF527 Bioinformatic Applications (/BF527/) What is 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 Things to know and remember about using web server-based tools You are using someone else’s computer You are (probably) getting a reduced set of options or capacity Servers are great for sporadic or proof-of-principle work, but for intensive work, the software should be obtained and run locally Five websites that all biologists should know NCBI (The National Center for Biotechnology Information; / 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) /PDB/ NCBI (/) Entrez interface to databases Medline/OMIM Genbank/Genpept/Structures BLAST server(s) Five-plus flavors of blast Draft Human Genome Much, much more… EBI (http://www.ebi.ac.uk/) SRS database interface EMBL, SwissProt, and many more Many server-based tools ClustalW, DALI, … SwissProt (http://expasy.cbr.nrc.ca/sprot/) Curation!!! Error rate in the information is greatly reduced in comparison to most other databases. Extensive cross-linking to other da