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Home > Problems > Chapter 3
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.
- 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.
- 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.
- Repeat the alignment with gap penalties of �5 and �1 and note the features of the alignment.
- 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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