D. mel. Proteins Track Settings
 
D. melanogaster (Apr. 2004 (BDGP R4/dm2)) Proteins   (All Genes and Gene Predictions tracks)

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Color elements: by score by D. mel. chromosome black

Label elements by: FlyBase Gene D. melanogaster mRNA D. melanogaster Position

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Data last updated at UCSC: 2005-06-25

Description

This track contains tBLASTn alignments of the peptides from the predicted and known genes identified in the D. melanogaster FlyBase as of 25 June 2005 to the A. mellifera sequence.

Methods

First, predicted proteins from the D. melanogaster FlyBase track were aligned with the D. melanogaster genome using the blat program to discover exon boundaries. Next, the amino acid sequences that make up each exon were aligned with the A. mellifera sequence using the tBLASTn program. Finally, the putative A. mellifera exons were chained together using an organism-specific maximum gap size but no gap penalty. The single best exon chains extending over more than 60% of the query protein were included. Exon chains that extended over 60% of the query and matched at least 60% of the protein's amino acids were also included.

Credits

tBLASTn is part of the NCBI Blast tool set. For more information on Blast, see Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-410.

Blat was written by Jim Kent. The remaining utilities required to produce this track were written by Jim Kent or Brian Raney.