Fugu Blat Track Settings
 
Fugu (Aug. 2002 (JGI 3.0/fr1)) Translated Blat Alignments   (All Comparative Genomics tracks)

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Assembly: Human May 2004 (NCBI35/hg17)
Data last updated at UCSC: 2004-07-23

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