Tools in bioinformatics. Fall 2009-10. Goals. Overview. To provide students with practical knowledge of bioinformatics tools and their application in research. Prerequisites. The course “Introduction to bioinformatics”
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Tools in bioinformatics
A class will be given every two weeks
There are three class groups:Sunday 16:00-18:00Monday 12:00-14:00
Computer classroom Sherman 03
When emailing your instructor (a question, your assignment, or whatever) please state in the “Subject” field: “Tools in Bioinfo”, IDs, CW/HW number (if relevant)
Yang X, Kurteva S, Ren X, Lee S, Sodroski J. “Subunit stoichiometry of human immunodeficiency virus type 1 envelope glycoprotein trimers during virus entry into host cells “, J Virol. 2006 May;80(9):4388-95.
Yang[AU] AND glycoprotein[TI] AND 2006[DP] AND J virol[TA]
For the full list of field tags: go to help -> Search Field Descriptions and Tags
Retrieve the publications of Yonath A, in the journals: Nature and Proc Natl Acad Sci U S A., in the last 5 years
Note: do not use the field Protein name [PROT], only GENE!
This time we directly search in the protein database
An explanation on GenBank records
> gi|10835167|ref|NP_000607.1| CD4 antigen precursor [Homo sapiens]MNRGVPFRHLLLVLQLALLPAATQGKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQKASSIVYKKEGEQVEFSFPLAFTVEKLTGSGELWWQAERASSSKSWITFDLKNKEVSVKRVTQDPKLQMGKKLPLHLTLPQALPQYAGSGNLTLALEAKTGKLHQEVNLVVMRATQLQKNLTCEVWGPTSPKLMLSLKLENKEAKVSKREKAVWVLNPEAGMWQCLLSDSGQVLLESNIKVLPTWSTPVQPMALIVLGGVAGLLLFIGLGIFFCVRCRHRRRQAERMSQIKRLLSEKKTCQCPHRFQKTCSPI
Save accession numbers for future use (makes searching quicker):RefSeq accession number: NP_000607.1
PDB ID 1G9M
HIV database http://hiv-web.lanl.gov/content/index
Total – N genes
Function f – K genes
Total – n genes
Function f – k genes
Is k/n > K/N, significantly ???
In a group of N genes there are K “special” ones
If we sample n genes out of N (without replacement), and found k “special” ones, would that be considered a random outcome?
Mathematically, we use the hypergeometric distribution to compute the probability of obtaining k or more “special” ones in a sample of n
21,121 siRNA knockdown assays, literally covering the entire coding-sequence part of the genome
273 HIV-dependency factors (HDFs) were discovered