We make a number of data files available (temporarily) on this site. The data files are as follows.
This is a bzip archive of an sqlite database containing the data we used during our probe design process and the probes that results from this process. The tables are:
This is a BED format file of the UCEs we located that are shared between chicken, lizard, and zebra finch. The locations within this file are relative to chicken (galGal3).
This is a BED format file of the locations of the probes we designed. The locations within this file are relative to chicken (galGal3).
This is a bzipped dump file of the mysql database in which we stored our alignments of each probe sequence to other genomes. Initially and for error checking purposes, we conducted the align, clean, and insert steps by hand (as seen in Simulation:steps). This process has now largely been automated in future:run_mutiple_lastz.py. The tables are:
all_orgs - this table contains data from all of the matches to individual species listed in probe matches to individual species
cons - this table is identical to the cons table from uce_probe.sqlite. it is repeated here for ease of use
group_XAB_5 - this contains the list of probes found in all members of
- monDom5
- loxAfr3
- choHof1
- hg19
- mm9
group_Bats_5 - this contains the list of probes found in all members of
- eriEur1
- equCab2
- bosTau4
- canFam2
- pteVam1
group_Bats_7 - this contains the list of probes found in all members of
- eriEur1
- equCab2
- bosTau4
- canFam2
- pteVam1
- myoLuc1
- ailMel1
group_Bats_8 - this contains the list of probes found in all members of
- eriEur1
- pteVam1
- myoLuc1
- bosTau4
- vicPac1
- equCab2
- canFam2
- ailMel1
group_Bats_12 - this contains the list of probes found in all members of
- eriEur1
- pteVam1
- myoLuc1
- bosTau4
- vicPac1
- susScr9
- oviAri1
- turTru1
- equCab2
- canFam2
- felCat3
- ailMel1
group_size_19 - this contains the list of probes found in all members of
- anoCar2
- bosTau4
- calJac3
- canFam2
- cavPor3
- chinese
- equCab2
- gorGor3
- hg19
- korean
- loxAfr3
- mm9
- monDom5
- oryCun2
- panTro2
- ponAbe2
- rheMac2
- taeGut1
- venter
group_size_23 - this contains the list of probes found in all memebrs of
- bosTau4
- canFam2
- cavPor3
- chinese
- dasNov2
- echTel1
- equCab2
- gorGor3
- hg19
- korean
- loxAfr3
- mm9
- monDom5
- ochPri2
- oryCun2
- panTro2
- ponAbe2
- pteVam1
- rn4
- speTri1
- tarSyr1
- tupBel1
- venter
group_size_25 - this contains the list of probes found in all members of
- anoCar2
- bosTau4
- calJac3
- canFam2
- cavPor3
- chinese
- dipOrd1
- equCab2
- gorGor3
- hg19
- korean
- loxAfr3
- mm9
- monDom5
- ornAna1
- oryCun2
- panTro2
- ponAbe2
- pteVam1
- rheMac2
- rn4
- taeGut1
- tarSyr1
- venter
- vicPac1
group_size_29 - this contains the list of probes found in all members of
- anoCar2
- bosTau4
- calJac3
- canFam2
- cavPor3
- chinese
- choHof1
- dipOrd1
- echTel1
- equCab2
- eriEur1
- gorGor3
- hg19
- korean
- loxAfr3
- mm9
- monDom5
- ornAna1
- oryCun2
- panTro2
- ponAbe2
- pteVam1
- rheMac2
- rn4
- taeGut1
- tarSyr1
- tupBel1
- venter
- vicPac1
probe_distribution - this contains a binary “matrix” indicating presence/absence (1/0) of probe matches by species
probes - this is a table providing the ids of the probes we designed
species - this table provides information on the genome build of each organism to which we aligned probes
sureselect - this table is identical to the probes table from uce_probe.sqlite
These tables provide the individual matches of probes to difference organisms, as found by using lastz to align our probe sequences to the individual genomes. We provide the build version, name, etc. of each genome sequence in the species table of the database dump described in group data tables.