-------- Original Message -------- Subject: attempted resolution of mismatches Date: Tue, 28 Oct 2008 12:51:06 +0000 I have tried to resolve the problems with the following FBgns (see notes below). Given the length of the peptide sequences I have used PAM30 and cranked up the expectation threshold on BLASTp. In all cases the peptides hit uniquely to a single protein with 100% identity. Many of the mismatches are due to the fact that our published FBgns are now secondary IDs. We should place our reference with the new, "primary" FBgn number and, if necessary, state that a secondary FBgn was used at the time of publication. Other than that, the situation or resolution for #6 is fairly straightforward (see below). Please let me know if you need any other information or clarification for any of these. 1. FBgn0037257 CG12584 CG34425 FBgn0085454 Gene split: blastp of 1 out of 2 aa sequences hits gene; other aa sequence has no hit Note: the 2 peptides uniquely hit FBgn0085454 and nothing else. FBgn0037257 is the secondary flybase ID. 2. FBgn0037799 CG12816 CG34107 FBgn0083943 Gene split: blastp of the aa sequence hits gene. Note: blastp hits FBgn0083943 with FBgn0037799 being the secondary ID. 3. FBgn0051722 CG17140 Gene split: blastp or tblastn of the aa sequence provides no hits Note: the single peptide hits FBgn0032306 with FBgn0051722 as the secondary ID. 4. FBgn0052316 CG33791 CG33791 FBgn0035240 Gene split: blastp of at least 1 aa sequence hits gene Note: peptides hit FBgn0035240 with FBgn0052316 being a secondary ID. 5. FBgn0052332 CG9130 Gene split: blastp or tblastn of the 2 aa sequences provides no hits Note: peptides hit FBgn0035197 with FBgn0052332 as a secondary ID. 6. FBgn0052918 CG15891 Unknown: can't find CG15891 amino acid in original paper. Note: the peptides are listed in the paper under CG15892 for some reason. CG15891 and CG15892 appear to be identical genes and both have the same synonym, CG32918. 7. FBgn0052940 Pif1 Pif1 FBgn0046874 Gene split: blastp of both aa sequences hits gene Note: peptides hit FBgn0046874 with FBgn0052940 as a secondary ID. 8. FBgn0052954 Adh Adh FBgn0000055 Gene split: blastp of 1 out of 2 aa sequences hits gene; other aa sequence has no hit Note: both peptides hit FBgn0000055 with 100% identity with FBgn0052954 as secondary ID. 9. FBgn0053188 CG33936 Gene split: blastp or tblastn of the aa sequence provides no hits Note: peptide hits CG33936 PB, PC and PD isoforms with 100% identity. No problem here. ---------------------------------------------------------- Dr. Steve Dorus RCUK Academic Fellow Lecturer in Evolutionary Biology Department of Biology and Biochemistry The University of Bath Bath, BA2 7AY ----------------------------------------------------------
