BIOL 311 Human Genetics Fall 2006 Lecture Bioinformatics Reading Chap 8 pp 221 224 Web Sites NCBI Baylor College of Medicine EMBL IDT Lecture Outline 1 Databases 2 Sequence utilities 3 BLAST 4 NCBI links Chromosome assemblies 5 Comparative genomics Lecture Bioinformatics Use of computers for storing and analyzing biological data especially DNA and protein sequences 1 Databases DNA GenBank US based data repository for DNA and protein sequences EMBL European database DDBJ Japanese database Organization of databases a sequence type genomic sequences cDNA sequences protein sequences b organism humans mouse mammals non mammals chicken Xenopus clawed frog Zebrafish Pufferfish Drosophila nematode C elegans plants Arabidopsis rice yeast Baker s yeast S cerevisiae bacteria viruses 1 c sequence quality draft sequence HTS vs final genomic sequences EST expressed sequence tags vs completed cDNAs Annotation of database Accession Gene product for cDNAs ESTs References Preparation of material subcloning vectors Sequence features exons open reading frame poly A addition sites 2 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 sites Protein sequences Secondary structure prediction Signal peptide prediction Post translational modification 3 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 0 E values depend on Bit score which incorporates sequence identities mismatched nucleotides gaps Length of query sequence Size of database 4 NCBI links human genome resources gene database dbSNP locus link entrez gene chromosome link map viewer 2