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1. A simple method that has been used for the prediction of orthologous proteins in two organisms is to search for a pair of sequences, a in organism 1 and b in organism 2, such that (1) a search of the proteome of 2 with a finds b as the best hit, and (2) a search of the proteome of 1 with b finds a as the best hit. The method is sometimes called the bidirectional best-hit method. The relationship is especially strong if the E value is very small (e.g., <10-20) and if an alignment of the proteins includes a majority of each sequence.

Prove that the above relationships hold for the yeast (Saccharomyces cerevisiae) cyclin 3 (CLB3) protein SwissProt no. P24870 and Caenorhabditis elegans protein no. Q10654 (gi|1705780). These highly conserved proteins regulate the cell cycle in eukaryotes at the point of transition between the G2 phase of the cell cycle and mitosis.

  1. Use the BLAST advanced options blastp and search the SwissProt protein database for proteins in the C. elegans (worm) proteome (choose from drop-down list of organisms). List the five best matches by E value, length of query, length of matched sequence, percent of query sequence in alignment, and percent of matched sequence in alignment.
  2. Repeat the above search using worm protein Q10654 to search the yeast proteome and record the same data.
  3. What evidence have you found that the yeast and worm proteins are orthologs?
  4. Describe the evolutionary origin of any other proteins that were matched in these searches to the query sequence.
  5. Briefly describe in one or two sentences how orthologous proteins can be better defined than by the above simple test.

2. Redraw Figure 11.11D, part a, with the mouse synteny block order reversed. Do not forget to change the sign of the mouse synteny blocks and the direction of the diagonals since their order is now reversed. Redraw the breakpoint graph in Figure 11.11D, part b, showing the number of cycles. Then calculate the number of rearrangements between the human and mouse X chromosomes as described in the Figure 11.11D legend.


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