## Description

This track shows blat translated protein alignments of the Fugu ($o_date) genome assembly to the $organism 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 $organism 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, W.J. BLAT - the BLAST-like alignment tool. Genome Res. 12(4), 656-664 (2002).