# 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 v4.7.2 Code/Executables, ontologies, motifs for HOMER http://homer.salk.edu/homer/data/software/homer.v4.7.2.zip ./ ORGANISMS arabidopsis v5.4 Arabidopsis thaliana (arabidopsis) accession and ontology information http://homer.salk.edu/homer/data/organisms/arabidopsis.v5.4.zip data/accession/ 3702,NCBI Gene chicken v5.4 Gallus gallus (chicken) accession and ontology information http://homer.salk.edu/homer/data/organisms/chicken.v5.4.zip data/accession/ 9031,NCBI Gene human v5.4 Homo sapiens (human) accession and ontology information http://homer.salk.edu/homer/data/organisms/human.v5.4.zip data/accession/ 9606,NCBI Gene rice v5.4 Oryza sativa (rice) accession and ontology information http://homer.salk.edu/homer/data/organisms/rice.v5.4.zip data/accession/ 39947,NCBI Gene pombe v5.4 Schizosaccharomyces pombe (pombe) accession and ontology information http://homer.salk.edu/homer/data/organisms/pombe.v5.4.zip data/accession/ 284812,NCBI Gene rat v5.4 Rattus norvegicus (rat) accession and ontology information http://homer.salk.edu/homer/data/organisms/rat.v5.4.zip data/accession/ 10116,NCBI Gene fly v5.4 Drosophila melanogaster (fly) accession and ontology information http://homer.salk.edu/homer/data/organisms/fly.v5.4.zip data/accession/ 7227,NCBI Gene laevis v5.4 Xenopus laevis (laevis) accession and ontology information http://homer.salk.edu/homer/data/organisms/laevis.v5.4.zip data/accession/ 8364,Kwon&Quigley zebrafish v5.4 Danio rerio (zebrafish) accession and ontology information http://homer.salk.edu/homer/data/organisms/zebrafish.v5.4.zip data/accession/ 7955,NCBI Gene mouse v5.4 Mus musculus (mouse) accession and ontology information http://homer.salk.edu/homer/data/organisms/mouse.v5.4.zip data/accession/ 10090,NCBI Gene yeast v5.4 Saccharomyces cerevisiae (yeast) accession and ontology information http://homer.salk.edu/homer/data/organisms/yeast.v5.4.zip data/accession/ 559292,NCBI Gene frog v5.4 Xenopus tropicalis (frog) accession and ontology information http://homer.salk.edu/homer/data/organisms/frog.v5.4.zip data/accession/ 8364,NCBI Gene worm v5.4 Caenorhabditis elegans (worm) accession and ontology information http://homer.salk.edu/homer/data/organisms/worm.v5.4.zip data/accession/ 6239,NCBI Gene PROMOTERS mouse-mRNA-5UTR v5.2 mouse refseq RNA 5'UTR http://homer.salk.edu/homer/data/promoters/mouse-mRNA-5UTR.v5.2.zip data/promoters/ mouse,mm9,refseq,0,0 chicken-mRNA v5.2 chicken refseq RNA http://homer.salk.edu/homer/data/promoters/chicken-mRNA.v5.2.zip data/promoters/ chicken,galGal4,refseq,0,0 arabidopsis v5.4 arabidopsis promoters (arabidopsis) http://homer.salk.edu/homer/data/promoters/arabidopsis.v5.4.zip data/promoters/ arabidopsis,tair10,orf,-2000,2000 human v5.3 human promoters (human) http://homer.salk.edu/homer/data/promoters/human.v5.3.zip data/promoters/ human,hg19,refseq,-2000,2000 yeast-mRNA-3UTR v5.2 yeast refseq RNA 3'UTR http://homer.salk.edu/homer/data/promoters/yeast-mRNA-3UTR.v5.2.zip data/promoters/ yeast,sacCer3,orf,0,0 fly v5.3 fly promoters (fly) http://homer.salk.edu/homer/data/promoters/fly.v5.3.zip data/promoters/ fly,dm3,refseq,-2000,2000 zebrafish-mRNA-3UTR v5.2 zebrafish refseq RNA 3'UTR http://homer.salk.edu/homer/data/promoters/zebrafish-mRNA-3UTR.v5.2.zip data/promoters/ zebrafish,danRer7,refseq,0,0 laevis v5.4 laevis promoters (laevis) http://homer.salk.edu/homer/data/promoters/laevis.v5.4.zip data/promoters/ laevis,laevis7.1,refseq,-2000,2000 frog-mRNA-5UTR v5.2 frog refseq RNA 5'UTR http://homer.salk.edu/homer/data/promoters/frog-mRNA-5UTR.v5.2.zip data/promoters/ frog,xenTro2,refseq,0,0 zebrafish-mRNA-5UTR v5.2 zebrafish refseq RNA 5'UTR http://homer.salk.edu/homer/data/promoters/zebrafish-mRNA-5UTR.v5.2.zip data/promoters/ zebrafish,danRer7,refseq,0,0 mouse v5.3 mouse promoters (mouse) http://homer.salk.edu/homer/data/promoters/mouse.v5.3.zip data/promoters/ mouse,mm9,refseq,-2000,2000 frog-mRNA v5.2 frog refseq RNA http://homer.salk.edu/homer/data/promoters/frog-mRNA.v5.2.zip data/promoters/ frog,xenTro2,refseq,0,0 frog v5.3 frog promoters (frog) http://homer.salk.edu/homer/data/promoters/frog.v5.3.zip data/promoters/ frog,xenTro2,refseq,-2000,2000 human-mRNA v5.2 human refseq RNA http://homer.salk.edu/homer/data/promoters/human-mRNA.v5.2.zip data/promoters/ human,hg19,refseq,0,0 chicken v5.3 chicken promoters (chicken) http://homer.salk.edu/homer/data/promoters/chicken.v5.3.zip data/promoters/ chicken,galGal4,refseq,-2000,2000 mouse-mRNA-3UTR v5.2 mouse refseq RNA 3'UTR http://homer.salk.edu/homer/data/promoters/mouse-mRNA-3UTR.v5.2.zip data/promoters/ mouse,mm9,refseq,0,0 rat v5.3 rat promoters (rat) http://homer.salk.edu/homer/data/promoters/rat.v5.3.zip data/promoters/ rat,rn5,refseq,-2000,2000 fly-mRNA-3UTR v5.2 fly refseq RNA 3'UTR http://homer.salk.edu/homer/data/promoters/fly-mRNA-3UTR.v5.2.zip data/promoters/ fly,dm3,refseq,0,0 mouse-mRNA v5.2 mouse refseq RNA http://homer.salk.edu/homer/data/promoters/mouse-mRNA.v5.2.zip data/promoters/ mouse,mm9,refseq,0,0 yeast-mRNA v5.2 yeast refseq RNA http://homer.salk.edu/homer/data/promoters/yeast-mRNA.v5.2.zip data/promoters/ yeast,sacCer3,orf,0,0 chicken-mRNA-5UTR v5.2 chicken refseq RNA 5'UTR http://homer.salk.edu/homer/data/promoters/chicken-mRNA-5UTR.v5.2.zip data/promoters/ chicken,galGal4,refseq,0,0 worm-mRNA-5UTR v5.2 worm refseq RNA 5'UTR http://homer.salk.edu/homer/data/promoters/worm-mRNA-5UTR.v5.2.zip data/promoters/ worm,ce10,refseq,0,0 yeast v5.3 yeast promoters (yeast) http://homer.salk.edu/homer/data/promoters/yeast.v5.3.zip data/promoters/ yeast,sacCer3,orf,-2000,2000 fly-mRNA v5.2 fly refseq RNA http://homer.salk.edu/homer/data/promoters/fly-mRNA.v5.2.zip data/promoters/ fly,dm3,refseq,0,0 pombe v5.4 pombe promoters (pombe) http://homer.salk.edu/homer/data/promoters/pombe.v5.4.zip data/promoters/ pombe,ASM294v2,orf,-2000,2000 chicken-mRNA-3UTR v5.2 chicken refseq RNA 3'UTR http://homer.salk.edu/homer/data/promoters/chicken-mRNA-3UTR.v5.2.zip data/promoters/ chicken,galGal4,refseq,0,0 human-mRNA-3UTR v5.2 human refseq RNA 3'UTR http://homer.salk.edu/homer/data/promoters/human-mRNA-3UTR.v5.2.zip data/promoters/ human,hg19,refseq,0,0 zebrafish v5.3 zebrafish promoters (zebrafish) http://homer.salk.edu/homer/data/promoters/zebrafish.v5.3.zip data/promoters/ zebrafish,danRer7,refseq,-2000,2000 worm-mRNA v5.2 worm refseq RNA http://homer.salk.edu/homer/data/promoters/worm-mRNA.v5.2.zip data/promoters/ worm,ce10,refseq,0,0 yeast-mRNA-5UTR v5.2 yeast refseq RNA 5'UTR http://homer.salk.edu/homer/data/promoters/yeast-mRNA-5UTR.v5.2.zip data/promoters/ yeast,sacCer3,orf,0,0 fly-mRNA-5UTR v5.2 fly refseq RNA 5'UTR http://homer.salk.edu/homer/data/promoters/fly-mRNA-5UTR.v5.2.zip data/promoters/ fly,dm3,refseq,0,0 worm-mRNA-3UTR v5.2 worm refseq RNA 3'UTR http://homer.salk.edu/homer/data/promoters/worm-mRNA-3UTR.v5.2.zip data/promoters/ worm,ce10,refseq,0,0 rat-mRNA v4.1 Rat RefSeq mRNA (rn4) http://homer.salk.edu/homer/data/promoters/rat-mRNA.v4.1.zip data/promoters/ rat,rn4,refseq,-2000,2000 rice v5.4 rice promoters (rice) http://homer.salk.edu/homer/data/promoters/rice.v5.4.zip data/promoters/ rice,IRGSP-1,name,-2000,2000 human-mRNA-5UTR v5.2 human refseq RNA 5'UTR http://homer.salk.edu/homer/data/promoters/human-mRNA-5UTR.v5.2.zip data/promoters/ human,hg19,refseq,0,0 worm v5.3 worm promoters (worm) http://homer.salk.edu/homer/data/promoters/worm.v5.3.zip data/promoters/ worm,ce10,refseq,-2000,2000 frog-mRNA-3UTR v5.2 frog refseq RNA 3'UTR http://homer.salk.edu/homer/data/promoters/frog-mRNA-3UTR.v5.2.zip data/promoters/ frog,xenTro2,refseq,0,0 zebrafish-mRNA v5.2 zebrafish refseq RNA http://homer.salk.edu/homer/data/promoters/zebrafish-mRNA.v5.2.zip data/promoters/ zebrafish,danRer7,refseq,0,0 GENOMES sacCer3 v5.4 yeast genome and annotation for UCSC sacCer3 http://homer.salk.edu/homer/data/genomes/sacCer3.v5.4.zip data/genomes/sacCer3/ yeast,default galGal4 v5.4 chicken genome and annotation for UCSC galGal4 http://homer.salk.edu/homer/data/genomes/galGal4.v5.4.zip data/genomes/galGal4/ chicken,default hg17 v5.4 human genome and annotation for UCSC hg17 http://homer.salk.edu/homer/data/genomes/hg17.v5.4.zip data/genomes/hg17/ human,default sacCer2 v5.4 yeast genome and annotation for UCSC sacCer2 http://homer.salk.edu/homer/data/genomes/sacCer2.v5.4.zip data/genomes/sacCer2/ yeast,default xenTro3 v5.4 frog genome and annotation for UCSC xenTro3 http://homer.salk.edu/homer/data/genomes/xenTro3.v5.4.zip data/genomes/xenTro3/ frog,default dm3 v5.4 fly genome and annotation for UCSC dm3 http://homer.salk.edu/homer/data/genomes/dm3.v5.4.zip data/genomes/dm3/ fly,default ASM294v2 v5.4 pombe genome and annotation (ASM294v2) http://homer.salk.edu/homer/data/genomes/ASM294v2.v5.4.zip data/genomes/ASM294v2/ pombe,default panTro3 v5.4 human genome and annotation for UCSC panTro3 http://homer.salk.edu/homer/data/genomes/panTro3.v5.4.zip data/genomes/panTro3/ human,default mm9 v5.4 mouse genome and annotation for UCSC mm9 http://homer.salk.edu/homer/data/genomes/mm9.v5.4.zip data/genomes/mm9/ mouse,default hg19 v5.4 human genome and annotation for UCSC hg19 http://homer.salk.edu/homer/data/genomes/hg19.v5.4.zip data/genomes/hg19/ human,default danRer7 v5.4 zebrafish genome and annotation for UCSC danRer7 http://homer.salk.edu/homer/data/genomes/danRer7.v5.4.zip data/genomes/danRer7/ zebrafish,default hg38 v5.4 human genome and annotation for UCSC hg38 http://homer.salk.edu/homer/data/genomes/hg38.v5.4.zip data/genomes/hg38/ human,default ce6 v5.4 worm genome and annotation for UCSC ce6 http://homer.salk.edu/homer/data/genomes/ce6.v5.4.zip data/genomes/ce6/ worm,default mm10 v5.4 mouse genome and annotation for UCSC mm10 http://homer.salk.edu/homer/data/genomes/mm10.v5.4.zip data/genomes/mm10/ mouse,default rn4 v5.4 rat genome and annotation for UCSC rn4 http://homer.salk.edu/homer/data/genomes/rn4.v5.4.zip data/genomes/rn4/ rat,default hg18 v5.4 human genome and annotation for UCSC hg18 http://homer.salk.edu/homer/data/genomes/hg18.v5.4.zip data/genomes/hg18/ human,default IRGSP-1 v5.4 rice genome and annotation (IRGSP-1) http://homer.salk.edu/homer/data/genomes/IRGSP-1.v5.4.zip data/genomes/IRGSP-1/ rice,default tair10 v5.4 arabidopsis genome and annotation (tair10) http://homer.salk.edu/homer/data/genomes/tair10.v5.4.zip data/genomes/tair10/ arabidopsis,default mm8 v5.4 mouse genome and annotation for UCSC mm8 http://homer.salk.edu/homer/data/genomes/mm8.v5.4.zip data/genomes/mm8/ mouse,default papAnu2 v5.4 human genome and annotation for UCSC papAnu2 http://homer.salk.edu/homer/data/genomes/papAnu2.v5.4.zip data/genomes/papAnu2/ human,default ce10 v5.4 worm genome and annotation for UCSC ce10 http://homer.salk.edu/homer/data/genomes/ce10.v5.4.zip data/genomes/ce10/ worm,default tetNig2 v5.4 tetraodon genome and annotation for UCSC tetNig2 http://homer.salk.edu/homer/data/genomes/tetNig2.v5.4.zip data/genomes/tetNig2/ tetraodon,default rn5 v5.4 rat genome and annotation for UCSC rn5 http://homer.salk.edu/homer/data/genomes/rn5.v5.4.zip data/genomes/rn5/ rat,default xenTro2 v5.4 frog genome and annotation for UCSC xenTro2 http://homer.salk.edu/homer/data/genomes/xenTro2.v5.4.zip data/genomes/xenTro2/ frog,default laevis7.1 v5.4 laevis genome and annotation (laevis7.1) http://homer.salk.edu/homer/data/genomes/laevis7.1.v5.4.zip data/genomes/laevis7.1/ laevis,default