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PART IV. COMPARING ALIGNMENT SCORES WITH SMALL AND LARGE GAP PENALTIES

For this question, use the program LALIGN on the University of Virginia FASTA server http://fasta.bioch.virginia.edu/. This program aligns sequences by a local dynamic programming algorithm and includes end gap penalties. It produces as many different alignments as specified, with no two alignments including a match of the same two sequence positions.

  1. Obtain the following two sequences from GenBank in FASTA format: recA.pro (P03017) from the bacterium E. coli and rad51.pro (P25454) from budding yeast (Saccharomyces cerevisiae). These proteins have the same function, i.e., promoting the pairing of homologous single-stranded DNAs. They almost certainly have the same three-dimensional structure but have diverged enough that they are difficult to align.
  2. Use LALIGN to align the above two sequences with gap penalties of 12 and 2. Note the length of the alignment, the percent identity, and the score of the alignment.
  3. Repeat the alignment with gap penalties of 5 and 1 and note the features of the alignment.
  4. Describe what happened when the gap penalties were reduced. Which of these alignments looks like a local alignment and which looks like a global alignment?




 

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