BSC4933(05)/ISC5224(01) Lab Report #7



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BSC4933(05)/ISC5224(01) Introduction to Bioinformatics Laboratory

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Lab Report #7

1) Did you have a difficult time deciding what sequences to include in your alignment? If so, describe the problems you had and how you resolved them. How many sequences did you end up with in your dataset?

2) What were the names of all of the PROSITE patterns found in your alignment? Do you think that they were all relevant to your molecular system, or where some of them likely false positives? If there were any false positives, what were their names?

3) Were you able to improve your alignment after its initial creation by PileUp? Did regional realignment help? Did you do any manual fine-tuning of your alignment?

4) What was the most similar sequence in your LookUp list to your HMM profile? What was its Expectation value? Was there a clear demarcation in scores between true, full-length homologues to your molecular system and other sequences? If there was, and if paralogues exist for your system, could you recognize where orthologues changed to paralogues, and then regardless of paralogues, where was the change to just motif similarity or mere background noise? What were the respective scores for these points?

5) What HMMerPfam domains were found in your sequence alignment, and what were their associated Expectation values? Were you surprised by the presence of any of these domains, why and which ones?

6) Tell me about your experience with SeaView, MAFFT, and T-Coffee: Did you like SeaView compared to SeqLab? Did MAFFT's EINSI mode compare well with your hand refined PileUp alignment; how about the FFTNS mode? What mode did MAFFT choose with its auto mode? Did you allow T-Coffee's M-Coffee mode to finish - how were those results?

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