hg19 syntenic ages
Authors/Creators
- 1. Vanderbilt University
- 2. University of California San Francisco
Description
# Hg19 46-way vertebrate tree syntenic block age files.
Information for hg19 46-way vertebrate multiple sequence alignment can be found here - http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/README.txt
# Scripts generating these files
(1) Creating syntenic block .bed files
https://github.com/slifong08/enh_ages/blob/54084ff12e521c20cc5288d6cb3590fac93c11ed/age_arch/manuscript_scripts/get_spec_count_msa-hg19.py
(2) Assigning most recent common ancestor (MRCA) and patristic distances to syntenic blocks
https://github.com/slifong08/enh_ages/blob/54084ff12e521c20cc5288d6cb3590fac93c11ed/age_arch/manuscript_scripts/get_synteny_age_hg19.py
### Bed file
# File columns
["chr", "start", "end", "strand", "reference_genome", "species_count", "length_synteny_block", "max_mrca", "max_patr"]
# Definitions
"max_mrca" = the phylogenetic distance from Homo sapiens to the most recent common ancestor of the oldest taxon.
"max_patr" = the phylogenetic distance from Homo sapiens to the oldest taxon.
"species_count" = the number of species' genomes the syntenic block maps to.
Files
Files
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