## Description

The Fugu v.3.0 whole genome shotgun assembly was provided by the US DOE Joint Genome Institute (JGI). The assembly was constructed with the JGI assembler, JAZZ, from paired end sequencing reads produced at JGI, Myriad Genetics, and Celera Genomics, resulting in a sequence coverage of 5.7X. All reads are plasmid, cosmid, or BAC end-sequences, with the predominant coverage derived from 2 Kb insert plasmids. This assembly contains 20,379 scaffolds totaling 319 million base pairs. The largest 679 scaffolds total 160 million base pairs.

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 the JGI Fugu rubripes website was used in the UCSC Genome Browser Fugu blat alignments. These data were freely provided 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).