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Introduction to databases - Practical

Introduction to databases - Practical. Query Sequence. >my weird new protein MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC KPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVV

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Introduction to databases - Practical

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  1. Introduction to databases - Practical

  2. Query Sequence >my weird new protein MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC KPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVV HFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQG SNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA

  3. 1. Do a InterProScan • http://www.ebi.ac.uk/Tools/services/web/toolform.ebi?tool=iprscanusing the sequence of interest • Clear all program options and then select only ‘FPrintscan’ and ‘PatternScan’ and then submit • Copy the image that is returned as the result summary for inclusion in your report • What is the putative function based on the patterns reported by Interpro?

  4. Now do a protein based BLAST search • (http://blast.ncbi.nlm.nih.gov/Blast.cgi) using the same sequence. • Discuss whether the results correspond with the pattern results in terms of predicted function. • Explain why these small motifs are so evolutionarily conserved that they can be used to predict what a protein’s function is?

  5. 3. Explore Entrez • Click through the ‘G’ link in the first BLAST result. Use as much information on the next page and links from it (HINT: Click the ‘OMIM’ link on the right hand side of the page) to answer the following, with a reasonable amount of detail: • What is this protein’s function in terms of its cellular role? • What disease(s) is it involved in when mutated? (HINT: there is more than one – look carefully)

  6. 4. Use the model organism databases • Use the Mouse Genome Database and check what physiological characteristics become apparent when the gene is experimentally disrupted: • Go to http://www.informatics.jax.org/ • Click on ‘Genes’ and do a Gene & Markers query using the gene symbol with the default settings • Scroll down to the ‘Alleles and Phenotype’ section and click on the linked number next to ‘All alleles’ • Do the experimental phenotypes agree with the diseases you found in (3)? Explain. • Would you have been able to get a good idea of the HUMAN gene’s cellular functions from the mouse information if you knew completely nothing about it? Explain.

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