# Homer Update File # # This file is updated from the Homer website and contains information about data available for # use with the program. # # This file has been further modified by the local update script # # Each section has the same format, which is separated values specifying: # package name version description url optional parameters (, separated) # SOFTWARE homer v4.11.1 Code/Executables, ontologies, motifs for HOMER http://homer.ucsd.edu/homer/data/software/homer.v4.11.1.zip ./ ORGANISMS anemone v6.3 Nematostella vectensis (anemone) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/anemone.v6.3.zip data/accession/ 45351,NCBI Gene arabidopsis v6.3 Arabidopsis thaliana (arabidopsis) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/arabidopsis.v6.3.zip data/accession/ 3702,NCBI Gene ascomycetes v6.0 Neurospora crassa (ascomycetes) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/ascomycetes.v6.0.zip data/accession/ 5141,NCBI Gene balbc_cocci v5.2 Balbc/J mouse and Coccidioides genome combined http://homer.ucsd.edu/homer/data/organisms/balbc_cocci.v5.2.zip data/accession/ balbc_cocci bee v6.3 Apis mellifera (bee) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/bee.v6.3.zip data/accession/ 7460,NCBI Gene chicken v6.3 Gallus gallus (chicken) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/chicken.v6.3.zip data/accession/ 9031,NCBI Gene chlamy v6.3 Chlamydomonas reinhardtii (chlamy) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/chlamy.v6.3.zip data/accession/ 3055,NCBI Gene ciliate v6.3 Tetrahymena thermophila (ciliate) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/ciliate.v6.3.zip data/accession/ 312017,NCBI Gene ciona v6.3 Ciona intestinalis (ciona) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/ciona.v6.3.zip data/accession/ 7719,NCBI Gene cocci v6.3 Coccidioides immitis RS (cocci) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/cocci.v6.3.zip data/accession/ 246410,NCBI Gene corn v6.3 Zea mays (corn) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/corn.v6.3.zip data/accession/ 4577,NCBI Gene cow v5.4 Bos taurus (cow) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/cow.v5.4.zip data/accession/ 9913,NCBI Gene diatom v6.3 Phaeodactylum tricornutum (diatom) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/diatom.v6.3.zip data/accession/ 556484,NCBI Gene dicty v6.3 Dictyostelium discoideum (dicty) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/dicty.v6.3.zip data/accession/ 352472,NCBI Gene dog v6.3 Canis lupus familiaris (dog) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/dog.v6.3.zip data/accession/ 9615,NCBI Gene fly v6.3 Drosophila melanogaster (fly) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/fly.v6.3.zip data/accession/ 7227,NCBI Gene frog v6.3 Xenopus tropicalis (frog) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/frog.v6.3.zip data/accession/ 8364,NCBI Gene fugu v6.3 Takifugu rubripes (fugu) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/fugu.v6.3.zip data/accession/ 31033,NCBI Gene human v6.3 Homo sapiens (human) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/human.v6.3.zip data/accession/ 9606,NCBI Gene hydra v6.3 Hydra vulgaris (hydra) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/hydra.v6.3.zip data/accession/ 6087,NCBI Gene laevis v6.3 Xenopus laevis (laevis) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/laevis.v6.3.zip data/accession/ 8355,NCBI Gene lamprey v6.3 Petromyzon marinus (lamprey) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/lamprey.v6.3.zip data/accession/ 7757,NCBI Gene mosquito v6.3 Anopheles gambiae (mosquito) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/mosquito.v6.3.zip data/accession/ 180454,NCBI Gene mouse v6.3 Mus musculus (mouse) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/mouse.v6.3.zip data/accession/ 10090,NCBI Gene mushroom v6.3 Agaricus bisporus (mushroom) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/mushroom.v6.3.zip data/accession/ 597362,NCBI Gene ncrassa v6.3 Neurospora crassa (ncrassa) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/ncrassa.v6.3.zip data/accession/ 367110,NCBI Gene patens v6.3 Physcomitrella patens (patens) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/patens.v6.3.zip data/accession/ 3218,NCBI Gene pig v6.3 Sus scrofa (pig) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/pig.v6.3.zip data/accession/ 9823,NCBI Gene pombe v6.3 Schizosaccharomyces pombe (pombe) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/pombe.v6.3.zip data/accession/ 4896,NCBI Gene pseudonana v6.3 Thalassiosira pseudonana (pseudonana) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/pseudonana.v6.3.zip data/accession/ 296543,NCBI Gene rat v6.3 Rattus norvegicus (rat) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/rat.v6.3.zip data/accession/ 10116,NCBI Gene rhesus v6.3 Macaca mulatta (rhesus) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/rhesus.v6.3.zip data/accession/ 9544,NCBI Gene rice v6.3 Oryza sativa (rice) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/rice.v6.3.zip data/accession/ 39947,NCBI Gene seahare v6.3 Aplysia californica (seahare) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/seahare.v6.3.zip data/accession/ 6500,NCBI Gene selaginella v6.3 Selaginella moellendorffii (selaginella) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/selaginella.v6.3.zip data/accession/ 88036,NCBI Gene tomato v6.3 Solanum lycopersicum (tomato) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/tomato.v6.3.zip data/accession/ 4081,NCBI Gene urchin v6.3 Strongylocentrotus purpuratus (urchin) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/urchin.v6.3.zip data/accession/ 7668,NCBI Gene volvox v6.3 Volvox carteri (volvox) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/volvox.v6.3.zip data/accession/ 3068,NCBI Gene worm v6.3 Caenorhabditis elegans (worm) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/worm.v6.3.zip data/accession/ 6239,NCBI Gene yeast v6.3 Saccharomyces cerevisiae (yeast) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/yeast.v6.3.zip data/accession/ 559292,NCBI Gene zebrafinch v6.3 Taeniopygia guttata (zebrafinch) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/zebrafinch.v6.3.zip data/accession/ 59729,NCBI Gene zebrafish v6.3 Danio rerio (zebrafish) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/zebrafish.v6.3.zip data/accession/ 7955,NCBI Gene PROMOTERS arabidopsis v6.3 arabidopsis promoters (arabidopsis) http://homer.ucsd.edu/homer/data/promoters/arabidopsis.v6.3.zip data/promoters/ arabidopsis,tair10,refseq,-2000,2000 chicken v5.5 chicken promoters (chicken) http://homer.ucsd.edu/homer/data/promoters/chicken.v5.5.zip data/promoters/ chicken,galGal4,refseq,-2000,2000 fly v5.5 fly promoters (fly) http://homer.ucsd.edu/homer/data/promoters/fly.v5.5.zip data/promoters/ fly,dm3,refseq,-2000,2000 frog v5.5 frog promoters (frog) http://homer.ucsd.edu/homer/data/promoters/frog.v5.5.zip data/promoters/ frog,xenTro2,refseq,-2000,2000 human v5.5 human promoters (human) http://homer.ucsd.edu/homer/data/promoters/human.v5.5.zip data/promoters/ human,hg19,refseq,-2000,2000 mouse v5.5 mouse promoters (mouse) http://homer.ucsd.edu/homer/data/promoters/mouse.v5.5.zip data/promoters/ mouse,mm9,refseq,-2000,2000 rat v5.5 rat promoters (rat) http://homer.ucsd.edu/homer/data/promoters/rat.v5.5.zip data/promoters/ rat,rn5,refseq,-2000,2000 worm v5.5 worm promoters (worm) http://homer.ucsd.edu/homer/data/promoters/worm.v5.5.zip data/promoters/ worm,ce10,refseq,-2000,2000 yeast v5.5 yeast promoters (yeast) http://homer.ucsd.edu/homer/data/promoters/yeast.v5.5.zip data/promoters/ yeast,sacCer3,orf,-2000,2000 zebrafish v5.5 zebrafish promoters (zebrafish) http://homer.ucsd.edu/homer/data/promoters/zebrafish.v5.5.zip data/promoters/ zebrafish,danRer7,refseq,-2000,2000 GENOMES AGPv3 v5.10 corn genome and annotation (AGPv3) http://homer.ucsd.edu/homer/data/genomes/AGPv3.v5.10.zip data/genomes/AGPv3/ corn,default anoGam1 v6.4 mosquito genome and annotation for UCSC anoGam1 http://homer.ucsd.edu/homer/data/genomes/anoGam1.v6.4.zip data/genomes/anoGam1/ mosquito,default apiMel2 v6.4 bee genome and annotation for UCSC apiMel2 http://homer.ucsd.edu/homer/data/genomes/apiMel2.v6.4.zip data/genomes/apiMel2/ bee,default apiMel3 v6.4 bee genome and annotation for UCSC apiMel3 http://homer.ucsd.edu/homer/data/genomes/apiMel3.v6.4.zip data/genomes/apiMel3/ bee,default aplCal1 v6.4 seahare genome and annotation for UCSC aplCal1 http://homer.ucsd.edu/homer/data/genomes/aplCal1.v6.4.zip data/genomes/aplCal1/ seahare,default canFam3 v6.4 dog genome and annotation for UCSC canFam3 http://homer.ucsd.edu/homer/data/genomes/canFam3.v6.4.zip data/genomes/canFam3/ dog,default ce10 v6.4 worm genome and annotation for UCSC ce10 http://homer.ucsd.edu/homer/data/genomes/ce10.v6.4.zip data/genomes/ce10/ worm,default ce11 v6.4 worm genome and annotation for UCSC ce11 http://homer.ucsd.edu/homer/data/genomes/ce11.v6.4.zip data/genomes/ce11/ worm,default ce6 v6.4 worm genome and annotation for UCSC ce6 http://homer.ucsd.edu/homer/data/genomes/ce6.v6.4.zip data/genomes/ce6/ worm,default ci2 v6.4 ciona genome and annotation for UCSC ci2 http://homer.ucsd.edu/homer/data/genomes/ci2.v6.4.zip data/genomes/ci2/ ciona,default ci3 v6.4 ciona genome and annotation for UCSC ci3 http://homer.ucsd.edu/homer/data/genomes/ci3.v6.4.zip data/genomes/ci3/ ciona,default corn.AGPv3 v5.10 corn genome and annotation (corn.AGPv3) http://homer.ucsd.edu/homer/data/genomes/corn.AGPv3.v5.10.zip data/genomes/corn.AGPv3/ corn,default danRer10 v6.4 zebrafish genome and annotation for UCSC danRer10 http://homer.ucsd.edu/homer/data/genomes/danRer10.v6.4.zip data/genomes/danRer10/ zebrafish,default danRer11 v6.4 zebrafish genome and annotation for UCSC danRer11 http://homer.ucsd.edu/homer/data/genomes/danRer11.v6.4.zip data/genomes/danRer11/ zebrafish,default danRer7 v6.4 zebrafish genome and annotation for UCSC danRer7 http://homer.ucsd.edu/homer/data/genomes/danRer7.v6.4.zip data/genomes/danRer7/ zebrafish,default dm3 v6.0 fly genome and annotation for UCSC dm3 http://homer.ucsd.edu/homer/data/genomes/dm3.v6.0.zip data/genomes/dm3/ fly,default dm6 v6.4 fly genome and annotation for UCSC dm6 http://homer.ucsd.edu/homer/data/genomes/dm6.v6.4.zip data/genomes/dm6/ fly,default fr3 v6.4 fugu genome and annotation for UCSC fr3 http://homer.ucsd.edu/homer/data/genomes/fr3.v6.4.zip data/genomes/fr3/ fugu,default galGal4 v6.4 chicken genome and annotation for UCSC galGal4 http://homer.ucsd.edu/homer/data/genomes/galGal4.v6.4.zip data/genomes/galGal4/ chicken,default galGal5 v6.4 chicken genome and annotation for UCSC galGal5 http://homer.ucsd.edu/homer/data/genomes/galGal5.v6.4.zip data/genomes/galGal5/ chicken,default galGal6 v6.4 chicken genome and annotation for UCSC galGal6 http://homer.ucsd.edu/homer/data/genomes/galGal6.v6.4.zip data/genomes/galGal6/ chicken,default gorGor3 v6.4 human genome and annotation for UCSC gorGor3 http://homer.ucsd.edu/homer/data/genomes/gorGor3.v6.4.zip data/genomes/gorGor3/ human,default gorGor4 v6.4 human genome and annotation for UCSC gorGor4 http://homer.ucsd.edu/homer/data/genomes/gorGor4.v6.4.zip data/genomes/gorGor4/ human,default gorGor5 v6.4 human genome and annotation for UCSC gorGor5 http://homer.ucsd.edu/homer/data/genomes/gorGor5.v6.4.zip data/genomes/gorGor5/ human,default hg17 v6.4 human genome and annotation for UCSC hg17 http://homer.ucsd.edu/homer/data/genomes/hg17.v6.4.zip data/genomes/hg17/ human,default hg18 v6.4 human genome and annotation for UCSC hg18 http://homer.ucsd.edu/homer/data/genomes/hg18.v6.4.zip data/genomes/hg18/ human,default hg19 v6.4 human genome and annotation for UCSC hg19 http://homer.ucsd.edu/homer/data/genomes/hg19.v6.4.zip data/genomes/hg19/ human,default hg38 v6.4 human genome and annotation for UCSC hg38 http://homer.ucsd.edu/homer/data/genomes/hg38.v6.4.zip data/genomes/hg38/ human,default mm10 v6.4 mouse genome and annotation for UCSC mm10 http://homer.ucsd.edu/homer/data/genomes/mm10.v6.4.zip data/genomes/mm10/ mouse,default mm8 v6.4 mouse genome and annotation for UCSC mm8 http://homer.ucsd.edu/homer/data/genomes/mm8.v6.4.zip data/genomes/mm8/ mouse,default mm9 v6.4 mouse genome and annotation for UCSC mm9 http://homer.ucsd.edu/homer/data/genomes/mm9.v6.4.zip data/genomes/mm9/ mouse,default panPan1 v6.4 human genome and annotation for UCSC panPan1 http://homer.ucsd.edu/homer/data/genomes/panPan1.v6.4.zip data/genomes/panPan1/ human,default panPan2 v6.4 human genome and annotation for UCSC panPan2 http://homer.ucsd.edu/homer/data/genomes/panPan2.v6.4.zip data/genomes/panPan2/ human,default panTro3 v6.4 human genome and annotation for UCSC panTro3 http://homer.ucsd.edu/homer/data/genomes/panTro3.v6.4.zip data/genomes/panTro3/ human,default panTro4 v6.4 human genome and annotation for UCSC panTro4 http://homer.ucsd.edu/homer/data/genomes/panTro4.v6.4.zip data/genomes/panTro4/ human,default panTro5 v6.4 human genome and annotation for UCSC panTro5 http://homer.ucsd.edu/homer/data/genomes/panTro5.v6.4.zip data/genomes/panTro5/ human,default panTro6 v6.4 human genome and annotation for UCSC panTro6 http://homer.ucsd.edu/homer/data/genomes/panTro6.v6.4.zip data/genomes/panTro6/ human,default papAnu2 v6.4 human genome and annotation for UCSC papAnu2 http://homer.ucsd.edu/homer/data/genomes/papAnu2.v6.4.zip data/genomes/papAnu2/ human,default patens.ASM242v1 v5.10 patens genome and annotation (patens.ASM242v1) http://homer.ucsd.edu/homer/data/genomes/patens.ASM242v1.v5.10.zip data/genomes/patens.ASM242v1/ patens,default petMar2 v6.4 lamprey genome and annotation for UCSC petMar2 http://homer.ucsd.edu/homer/data/genomes/petMar2.v6.4.zip data/genomes/petMar2/ lamprey,default petMar3 v6.4 lamprey genome and annotation for UCSC petMar3 http://homer.ucsd.edu/homer/data/genomes/petMar3.v6.4.zip data/genomes/petMar3/ lamprey,default rheMac2 v6.4 rhesus genome and annotation for UCSC rheMac2 http://homer.ucsd.edu/homer/data/genomes/rheMac2.v6.4.zip data/genomes/rheMac2/ rhesus,default rheMac3 v6.4 rhesus genome and annotation for UCSC rheMac3 http://homer.ucsd.edu/homer/data/genomes/rheMac3.v6.4.zip data/genomes/rheMac3/ rhesus,default rheMac8 v6.4 rhesus genome and annotation for UCSC rheMac8 http://homer.ucsd.edu/homer/data/genomes/rheMac8.v6.4.zip data/genomes/rheMac8/ rhesus,default rice.IRGSP-1.0 v5.10 rice genome and annotation (rice.IRGSP-1.0) http://homer.ucsd.edu/homer/data/genomes/rice.IRGSP-1.0.v5.10.zip data/genomes/rice.IRGSP-1.0/ rice,default rn4 v6.4 rat genome and annotation for UCSC rn4 http://homer.ucsd.edu/homer/data/genomes/rn4.v6.4.zip data/genomes/rn4/ rat,default rn5 v6.4 rat genome and annotation for UCSC rn5 http://homer.ucsd.edu/homer/data/genomes/rn5.v6.4.zip data/genomes/rn5/ rat,default rn6 v6.4 rat genome and annotation for UCSC rn6 http://homer.ucsd.edu/homer/data/genomes/rn6.v6.4.zip data/genomes/rn6/ rat,default sacCer2 v6.4 yeast genome and annotation for UCSC sacCer2 http://homer.ucsd.edu/homer/data/genomes/sacCer2.v6.4.zip data/genomes/sacCer2/ yeast,default sacCer3 v6.4 yeast genome and annotation for UCSC sacCer3 http://homer.ucsd.edu/homer/data/genomes/sacCer3.v6.4.zip data/genomes/sacCer3/ yeast,default strPur2 v6.0 urchin genome and annotation for UCSC strPur2 http://homer.ucsd.edu/homer/data/genomes/strPur2.v6.0.zip data/genomes/strPur2/ urchin,default susScr11 v6.4 pig genome and annotation for UCSC susScr11 http://homer.ucsd.edu/homer/data/genomes/susScr11.v6.4.zip data/genomes/susScr11/ pig,default susScr3 v6.4 pig genome and annotation for UCSC susScr3 http://homer.ucsd.edu/homer/data/genomes/susScr3.v6.4.zip data/genomes/susScr3/ pig,default taeGut2 v6.4 zebrafinch genome and annotation for UCSC taeGut2 http://homer.ucsd.edu/homer/data/genomes/taeGut2.v6.4.zip data/genomes/taeGut2/ zebrafinch,default tair10 v6.0 arabidopsis genome and annotation (tair10) http://homer.ucsd.edu/homer/data/genomes/tair10.v6.0.zip data/genomes/tair10/ arabidopsis,default tetNig2 v6.4 fugu genome and annotation for UCSC tetNig2 http://homer.ucsd.edu/homer/data/genomes/tetNig2.v6.4.zip data/genomes/tetNig2/ fugu,default xenTro2 v6.4 frog genome and annotation for UCSC xenTro2 http://homer.ucsd.edu/homer/data/genomes/xenTro2.v6.4.zip data/genomes/xenTro2/ frog,default xenTro3 v6.4 frog genome and annotation for UCSC xenTro3 http://homer.ucsd.edu/homer/data/genomes/xenTro3.v6.4.zip data/genomes/xenTro3/ frog,default xenTro7 v6.4 frog genome and annotation for UCSC xenTro7 http://homer.ucsd.edu/homer/data/genomes/xenTro7.v6.4.zip data/genomes/xenTro7/ frog,default xenTro9 v6.4 frog genome and annotation for UCSC xenTro9 http://homer.ucsd.edu/homer/data/genomes/xenTro9.v6.4.zip data/genomes/xenTro9/ frog,default