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Practical Bioinformatics: Analyzing Protein Sequence for Function and Structure

Added on -2019-09-20

This article teaches how to analyze a protein sequence by bioinformatics methods to determine its function and structure. It covers methods like BLAST, FASTA, PSI-BLAST, PROSITE, PRINTS, BLOCKS, Pfam, and more to predict protein function and structure from sequence. The article also discusses how to make multiple alignments, phylogenetic trees, and predict secondary and tertiary structures. It also covers how to predict trans-membrane segments and protein-protein interactions.
| 3 pages
| 671 words

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Practical Bioinformatics 80% 3800 words Introduction:You are required to analyse a protein sequence by bioinformatics methods. What is its likely function? If it does not have a structurecan you determine a model for the structure? What does the model tell you about its function? It might also be a "hypothetical"protein, where the structure has already been determined by a structural genomics consortium. In which case can you use sequence and known structure to determine protein function? Youare not restricted to methods covered in the lectures, but you should focus on methods with the general aim of prediction of protein function and/or structure from sequence.Protein sequence:MSPSVEETTS VTESIMFAIV SFKHMGPFEG YSMSADRAAS DLLIGMFGSV SLVNLLTIIGCLWVLRVTRP PVSVMIFTWN LVLSQFFSIL ATMLSKGIML RGALNLSLCR LVLFVDDVGLYSTALFFLFL ILDRLSAISY GRDLWHHETR ENAGVALYAV AFAWVLSIVA AVPTAATGSLDYRWLGCQIP IQYAAVDLTI KMWFLLGAPM IAVLANVVEL AYSDRRDHVW SYVGRVCTFYVTCLMLFVPY YCFRVLRGVL QPASAAGTGF GIMDYVELAT RTLLTMRLGI LPLFIIAFFSREPTKDLDDS FDYLVERCQQ SCHGHFVRRL VQALKRAMYS VELAVCYFST SVRDVAEAVKKSSSRCYADA TSAAVVVTTT TSEKATLVEH AEGMASEMCP GTTIDVSAES SSVLCTDGENTVASDATVTA LThere should be an abstract of up to 250 words. An introduction, detailing what you have done, and why it is interesting, perhaps with a brief literature review if relevant.You are not expected to give details for the methods you have used, but do cite primary references if you use them. The remainder of the paper should be:Results and Discussion section giving relevant results and discussing their significance;Conclusions section where you review the significance of your results and comment on the usefulness of the methods used;References.Marks will be awarded as follows:Abstract (5%) - awarded for a clear and concise abstract of the paper.

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