Answers to Assignment 2
Human carrier sequences that do not have a mouse ortholog The class has all completed two mouse orthologs of human carriers that did not have a known ortholog identified beforehand. These have been added into the sequence alignment of carriers that we used at the beginning. This alignment now has 286 sequences in it, 51 are human and 49 are mouse. There is evidence for alternative splicing in some of the sequences. The files have been updated to include all the new sequences and the blast server for carriers has also been updated. One benefit of doing this project was the discovery of two mouse sequences that did not match very well to known human carriers. I did blast searches with these new mouse sequences against the human HTGS section and found two new human carriers that were not identified before. These are now called 78H and 198D. I encourage you to try the optional problem 1 given under module 3. It will help you later when we work on assembling genes from genomic fragments. Rob Edwards is trying to do an assembly of the the Ciona genome from 4.3 million sequence reads. The first program has been running for over a week and there are more steps to be done. If he is successful, we will attempt to find every P450 gene in Ciona and assemble these genes. There should be less than 50, so each student should do two, but they should not be the same two. We can work that out early in the process by identifying accession numbers and making sure no one is working on the same accession numbers. D. Nelson 2/26/02