The Fugu whole genome shotgun assembly was constructed with the JGI assembler, JAZZ, paired end sequencing reads at a coverage of 5.7X produced at JGI, Myriad Genetics, and Celera Genomics. All reads are plasmid, cosmid, or BAC end-sequences, with the predominant coverage coming from 2 kb insert plasmids. The assembly contains 20,379 scaffolds totaling 319 million base pairs; the largest 679 scaffolds total 160 million base pairs. Gene modeling and analysis were performed at JGI, Singapore, Cambridge, and the Institute for Systems Biology.
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 -+.
The alignments were done with blat in translated protein mode requiring 2 nearby 4-mer matches to trigger a detailed alignment. The $organism genome was masked with RepeatMasker and Tandem Repeat Finder before running blat.
The 3.0 draft from http://genome.jgi-psf.org/fugu6/fugu6.info.html was used in the UCSC Fugu blat alignments. This data has been provided freely by the DOE Joint Genome Institute for use in this publication only.