Bioinformatics

Bioinformatics Homework. : Why the “once a gap, always a gap” rule? Is it an insertion or a deletion? Does it matter?

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Bioinformatics Homework. 1.Why the “once a gap, always a gap” rule? Is it an insertion or a deletion? Does it matter? 2.Why might there be a bacterial homolog? What about the gap? How would you handle the “gap penalty?” 3.Find out what you can about Clustal Omega. 4.For those more familiar with HMMs, try to … Read more

Based on the colors and the distribution, from which of the three domains of life are the majority of hits?The proteasome sequence is from a hyperthermophilic archaeon. Why do you suppose there may be a (relative) lack of total hits in archaea using HMMER?

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Bioinformatics 1. 1. Run a Delta-BLAST with the silkworm insulin protein (P26726). Limit to human proteins in the RefSeq_Protein database. a. How many total sequences? b. How many human homologs appear to have the insulin domain (irrespective of the e-value threshold)? c. Now edit search remove the human from the organism selection and change DELTA-BLAST … Read more