BSC4933(04)/ISC5224(01) Lab Report #7



	School of Computational Science supported course

Steve's FSU links

Steve's Home Page

Steve's SCS TWiki BioInfo' Portal

An Introduction to Bioinformatics Laboratory

GCG Workshops

School of Computational Science

Biology Department

westcott building

BSC4933(04)/ISC5224(01) Introduction to Bioinformatics Laboratory

Name:
E-Mail:

Lab Report #7

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

2) What were the names of all of the PROSITE patterns found in your protein sequence that was used (top-most in SeqLab)? 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) Did you try to improve your protein alignment after its initial creation by ClustalW? Did you do any manual fine-tuning of your alignment? Describe what you did.

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 ClustalW 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?

Press when you have completed this form, or press to clear all fields and start over.




Steve's Home \| Workshop Page \| SCS \| Biology \| copyright © 2009 Steven M. Thompson, stevet@bio.fsu.edu