Description
This track contains tBLASTn alignments of the peptides from the WormBase
gene annotations on C. elegans version WS190 (UCSC ce6).
Methods
First, the predicted proteins from the C. elegans WormBase Genes track
were aligned to the C. elegans genome using the blat program to
discover exon boundaries. Next, the amino acid sequences that make up each
exon were aligned with the C. remanei sequence using the tBLASTn
program. Finally, the putative C. remanei exons were chained together
using a maximum gap size of 50,000 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
used to produce this track were written by Jim Kent, Brian Raney and
Hiram Clawson.
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