BIOL 311 Human Genetics Fall 2006Lecture: BioinformaticsReading: Chap. 8 pp. 221-224Web Sites: NCBI, Baylor College of Medicine, EMBL, IDTLecture Outline:1. Databases2. Sequence utilities3. BLAST4. NCBI links: Chromosome assemblies5. Comparative genomicsLecture:Bioinformatics: Use of computers for storing and analyzing biological data, especially DNA and protein sequences.1. DatabasesDNA: GenBank--US-based data repository for DNA and protein sequencesEMBL: European databaseDDBJ: Japanese databaseOrganization of databasesa. sequence type:genomic sequencescDNA sequencesprotein sequencesb. organismhumansmousemammalsnon-mammals- chicken- Xenopus (clawed frog)- Zebrafish- PufferfishDrosophilanematode: C. elegansplants: Arabidopsis, riceyeast: Baker's yeast=S. cerevisiaebacteriaviruses1c. sequence qualitydraft sequence (HTS) vs. final genomic sequencesEST (expressed sequence tags) vs. completed cDNAsAnnotation of database- Accession #- Gene product for cDNAs, ESTs- References- Preparation of material/subcloning/vectors- Sequence features- exons, open reading frame, poly(A) addition sites2. Sequence analysis"utilities", see BCM Search Launcher, Baylor College of Medicine- DNA sequences- Restriction site analysis- Complement- Translation- Primer design: see IDT web site- DNA sequence assembly (need specialized software such as Vector NTI)- Transcription factor binding sitesProtein sequences- Secondary structure prediction- Signal peptide prediction- Post-translational modification3. Blast=basic local sequence alignment tool- most powerful bioinformatics tool of all- enables comparison of DNA sequences (BLASTN)- DNA sequences translated compared to protein database (BLASTX)E-value=expected value- # of alignments you expect to find by chance- biologically significant values have E-values <<<< 1.0E-values depend on- Bit score, which incorporates # sequence identities, # mismatched nucleotides, # gaps- Length of query sequence - Size of database4. NCBI links- human genome resources- gene database- dbSNP- locus link  entrez gene- chromosome link, map