CHEM 402 HW 4

CHEM 402 Chemical Information Systems Fall 2024

Homework 4

Wednesday, November 27, 2024, at 1:00 PM To be submitted by 9:00 AM via BlackBoard

Get the protein sequences for human IRGM (Accession: NP_001139277.1) and the rat IRGM (Accession: NP_001012007.1). You may use the Entrez Protein Search at the NCBI website (http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein) to fetch the sequences. On the detailed protein information page, you may use the FASTA link at the top of the page to get the sequences in the FASTA format. Compare the local alignment of these sequences under dynamic programming. You may use the SIM tool by ExPasy (http://www.expasy.org/tools/sim-prot.html) to align the sequences. a) (5 points) Note the effect of varying open and extended gap penalties on the alignment. Report the top-5 local alignment scores obtained using BLOSUM62 on the following pair of (open, extend) penalties: (12,12), (12,4), (12,1), (8,1), (4,1). Just write down the scores and the lengths of the alignments; you do not need to show the actual alignment. b) (5 points) Which pair of (open, extended) penalties given in part (a) corresponds to the linear gap model? c) (5 points) Now align the human IRGM to chimpanzee IRGM (Accession: XP_527077.1) with the default parameters (BLOSUM62, Gap Open: 12, Gap Extend: 4). Compare this alignment with that between human and rat IRGM (using same parameters) in terms of length and score. Are the conserved sites between humans and mice also conserved between humans and chimpanzees?