Description
This track shows blat translated protein alignments of the Fugu
(Aug. 2002 (JGI 3.0/fr1)) genome assembly to the human genome. The
v3.0 Fugu whole genome shotgun assembly was provided by the
US
DOE Joint Genome Institute (JGI).
The strand information (+/-) for this track is in two parts. The
first + or - indicates the orientation of the query sequence whose
translated protein produced the match. The second + or - indicates the
orientation of the matching translated genomic sequence. Because the two
orientations of a DNA sequence give different predicted protein sequences,
there are four combinations. ++ is not the same as --; nor is +- the same
as -+.
Methods
The alignments were made with blat in translated protein mode requiring two
nearby 4-mer matches to trigger a detailed alignment. The human
genome was masked with RepeatMasker and Tandem Repeat Finder before
running blat.
Credits
The
3.0 draft from JGI was used in the
UCSC Fugu blat alignments. These data were provided freely by the JGI
for use in this publication only.
References
Kent WJ.
BLAT - the BLAST-like alignment tool.
Genome Res. 2002 Apr;12(4):656-64.
PMID: 11932250; PMC: PMC187518
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