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Exploring Protein Function and Genetic Links Through Bioinformatics Tools

In this guide, we delve into the analysis of a novel protein sequence using bioinformatics tools. By employing InterProScan for motif analysis, we identify potential functional patterns and correlate them with BLAST search results. We also investigate relevant functionality using the Mouse Genome Database to understand physiological characteristics associated with gene disruptions. This comprehensive approach helps illuminate the cellular roles of proteins and their implications in various diseases, offering insights into evolutionary conservation of motifs as predictive tools for protein function.

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Exploring Protein Function and Genetic Links Through Bioinformatics Tools

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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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