2 Biolobical Databases

2 Biolobical Databases - 1 Introduction to Bioinformatics/...

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1 Introduction to Bioinformatics/ Elements of Bioinformatics Biological Databases
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2 References • Baxevanis, A.D., and Ouellette, B.F.F. (2005) Bioinformatics - A practical guide to the analysis of genes and proteins (3rd ed). John Wiley and Sons, NY. Chapter 1 and Chapter 3. • Mount, D.W. (2004) Bioinformatics: Sequence and Genome Analysis (2nd ed). Cold Spring Harbor Lab. Press, N.Y. Chapter 2.
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3 First issue of each year’s Nucleic Acids Research is devoted to the description of biological databases (http://http://nar.oxfordjournals.org/) List of biological databases List of bioinformatics servers
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4 1170 databases were catalogued in 2009 http://www.oxfordjournals.org/nar/database/c
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5 http://bioinformatics.ca/links_directory/ A compilation of bioinformatics web servers
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6 DNA Databanks • The International Nucleotide Sequence Database Collaboration (http://www.insdc.org/): – Collaboration between GenBank, EMBL and DDBJ – Almost complete synchronization between databases
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7 EBI GenBank GenBank DDBJ DDBJ EMBL EMBL EMBL EMBL Entrez SRS getentry NIG NIG CIB NCBI NIH NIH •Submissions •Updates •Submissions •Updates •Submissions •Updates International Sequence Database Collaboration
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8 GenBank • There are approximately 9.5 x 10 10 bases in 9.3 x 10 7 sequence records in the traditional GenBank as of August 2008. • Divided into subsets that roughly correspond to taxonomic groups http://www.ncbi.nlm.nih.gov/Genbank/)
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9 GenBank • GenBank divisions: – PRI primate sequences – ROD rodent sequences – MAM other mammalian sequences – VRT other vertebrate sequences – INV invertebrate sequences – PLN plant, fungal, and algal sequences – BCT bacterial sequences – VRL viral sequences – PHG bacteriophage sequences – SYN synthetic sequences (cloning vectors) – UNA unannotated sequences – CON constructed sequences
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10 GenBank • GenBank divisions: – EST EST sequences (expressed sequence tags) – STS STS sequences (sequence tagged sites) – GSS
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2 Biolobical Databases - 1 Introduction to Bioinformatics/...

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