Description
These tracks display conserved non-coding elements from genomic 4-way phastcons (zebrafish, grass carp, common carp and goldfish).
Display Conventions and Configuration
This track display the conserved region in bed format.
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
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US Server