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| 1) Viral reverse transcriptases, such as the pol gene
product encoded by HIV-1, have human homologs. The GenBank accession number for
HIV-1 reverse transcriptase is NP_057849. This sequence is similar to human
protein (accession number P10266). Use blast2 to perform pairwise alignment.
Obtain the bit score, E value, percent identity, gap penalty parameters (gap
opening and gap extension), and percent of gaps in the alignment. Vary the
scoring matrix and list these output parameters again. Complete the table below.
Justify any changes in the output parameters. Scoring matrix Score E value Identity Gap Penalties Gaps BLOSUM62 BLOSUM45 BLOSUM80 PAM30 PAM70 2) Search the protein database in NCBI to find the C-terminal region (approximately 215 residues) of human BRCA1 (SWISS-PROT accession number P38398). Search the NR protein database with this sequence using PSI-BLAST. Save your search results. Now perform a second iteration. Compare your new search results. Some sequence alignments from the second search have higher scores than the same sequence alignment obtained from the first search. Why? Alternatively, some sequence alignments from the second search have lower scores than the same sequence alignments obtained from the first search. Why? |
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