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Dorus, S. (2008.10.28). Resolution of Dorus et al. (2006) gene mismatches. 
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-------- Original Message --------
 Subject:     attempted resolution of mismatches
 Date:     Tue, 28 Oct 2008  12:51:06  +0000
 From:     Steve Dorus <sd236@XXXX>
 To:     Rob Kulathinal <rob@XXXX>
 CC:     Timothy Karr <tkarr@XXXX>
 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, Ć¢  primaryĆ¢   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
Related Publication(s)
Research paper

Genomic and functional evolution of the Drosophila melanogaster sperm proteome.
Dorus et al., 2006, Nat. Genet. 38(12): 1440--1445 [FBrf0191959]

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