.
For the same sequences used, calculate the alignment
matrix with traceback using alpha = beta = 5, Match score= 10, and
Mismatch Penalty score = 10. Compare your optimal alignments with those
from.
.
Download sequences contained in accession numbers P21189 and
NP 143776.1 from the NCBI GenBank database. Using the alignment server
available at http://www.cmb.usc.edu, perform the following alignments.
a. Perform global alignment using “blosum62” as the penalty matrix (see
Section 7.5.2) and the default indel settings (alpha = 15, beta = 3).
Examine your result: Can you discern a region that likely will produce a
high-scoring local alignment?
b. Perform local alignment on the same sequences. Did the result from local
alignment agree with your prediction based upon the global alignment?
c. Use the contiguous sequence from 1Q8I (remove indels) that resulted from
the local alignment with NP 143776.1 as query for an NCBI BLAST search
(Chapter 7) of the non-redundant databases. Are any putative conserved
domains found? Check your output to see whether there are significant
hits to Danio or Arabidopsis sequences.