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IST 444 Assignments

IST 444 FADD

Pairwise Assignment

NM_001095548 

NM_010175 

NP_00381

NP_001089017 

NP_034305    

Discuss the three Programs below and select whether nucleic acid analysis or protein analysis was most informative for your gene of interest.

The protein analysis seems to be the best for the gene because there is higher percent identities and similarities.Although the nucleic acid analysis was consistent throughout the procedure, the protein analysis gave a more concise and accurate read.

Which method worked best with the closely related sequence (most alignment, fewest gaps)?

Best Fit was the best method for the closely related sequences. The percent similarity was 76.8% and the percent identity was 69.5%. There are zero gaps for the human to house mouse peptide sequences.

Which worked best with the distantly related sequences (most alignment, fewest gaps)?

Best fit was the best method for the distantly related sequences. The percent similarity was 53.2% and percent identity was 42.1%. The number of gaps were 4. Although this may seem high, the gaps for GAP method was greater than 4.

BestFit
Makes an optimal alignment of the best segment of similarity between two sequences. Optimal alignments are found by inserting gaps to maximize the number of matches using the local homology algorithm of Smith and Waterman.

Compare
Compares two peptide or nucleic acid sequences and creates a graph that shows where the two sequences are similar.

Gap
Uses the algorithm of Needleman and Wunsch to find the alignment of two complete sequences. It maximizes the number matches and minimizes the number of gaps.