Description

These tracks display genomic 4-way (zebrafish, grass carp, common carp and goldfish) phastcons scores.

Display Conventions and Configuration

This track display the phastcons score for each position. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the "Graph configuration help" link for an explanation of the configuration options.

Methods

All-to-all pairwise genomic alignment was performed using lastz (--gapped --ambiguous=n --step=3 --strand=both --masking=100 --maxwordcount=100 --identity=70..100 --format=axt), axtToChain (‘-faQ -faT -minScore=3000 -linearGap=medium) and chainNet (-minScore=5000) for four species (goldfish, common carp, grass carp, zebrafish) and transform to pairwise MAF format, split at gaps longer than 30bp (chainToAxt –maxGap=30, then axtToMaf -score). All the pairwise MAF files were transformed to multiple alignment MAF files using roast (P=multic). Phylogenetic model were fit for each chromosome, linkage group or scaffold using phyloFit (http://compgen.cshl.edu/phast/) (--tree '(ZF,(GC,(GF,CC)))' --subst-mod REV --nrate 4), which was used by phastCons for computing conserve score and regions.

Credits

These data were produced by the Developmental Genomics Section and the NIH Intramural Sequencing Center at the National Human Genome Research Institute. For questions, please email Shawn Burgess or Zelin Chen.

References