euGenes/Arthropods About Arthropods EvidentialGene DroSpeGe
Protein and CDS sequence fasta files of fish species genes used for OrthoMCL orthology of the 'fish12' analysis.

The fasta files include OrthoGroupID with each sequence header, as dbxref=euGenes:FISH12I_Gnnnn, e.g. fish12.astymex.aa,cds
>astymex:ENSAMXP00000000002 dbxref=euGenes:FISH12I_G20243; pep:novel gene:ENSAMXG00000000003 transcript:ENSAMXT00000000002
MEKETSPLCAADIIAELKRKFAFLSGGRGQDGSPIIIFPEFTSFGEIGDQEFHNVLTYLT

OrthoGroupID form is "euGenes:FISH12I_Gnnnn" where nnn group number corresponds to the fish12_omcl/ tables,
fish12a_omclgn.tab: OrthoGroupID, ProteinID
fish12a-orthomcl-count.tab: OrthoGroup# .. gene counts/species
fish12a_genes.ugp*: OrthoGroupID, annotations

The idtab files have corresponding ID columns as: ProteinID, OrthoGroupID, GeneID, TranscriptID

The .aa and .cds fasta files have genes with same ID (the protein ID). Several of these source files are Ensembl CDS where Transcript ID (ENS..T) was replaced with Protein ID (ENS..P). Sequences include only the primary transcript form. Names files are the name taken from sequence or associated annotation.

The following are sourced from Ensembl release 74 (pep.all.fa and cds.all.fa) ,
astymex = Astyanax_mexicanus.AstMex102 ; zebrafish = Danio_rerio.Zv9 ; stickleback = Gasterosteus_aculeatus.BROADS1 ; spotgar = Lepisosteus_oculatus.LepOcu1 ; tilapia = Oreochromis_niloticus.Orenil1.0 ; medaka = Oryzias_latipes.MEDAKA1 ; tetraodon = Tetraodon_nigroviridis.TETRAODON8 ; platyfish = Xiphophorus_maculatus.Xipmac4.4.2 ;

mayzebr is from NCBI genomes/Maylandia_zebra/ protein and rna genbank releases. Catfish is Evigene mRNA assembly from EvidentialGene/vertebrates/catfish/ Killifish is from this project (Evigene genome-genes + mRNA-assembly)


      Name                        Last modified       Size  

[DIR] Parent Directory 04-Jul-2015 14:05 - [   ] fish12.astymex.aa.gz 22-Mar-2014 15:22 8.2M [   ] fish12.astymex.cds.gz 22-Mar-2014 17:36 13.5M [TXT] fish12.astymex.idtab 22-Mar-2014 17:05 1.7M [   ] fish12.astymex.names.gz 23-Mar-2014 02:13 318k [   ] fish12.catfish.aa.gz 22-Mar-2014 15:22 10.7M [   ] fish12.catfish.cds.gz 23-Mar-2014 00:04 16.9M [TXT] fish12.catfish.idtab 23-Mar-2014 02:02 3.0M [   ] fish12.human.aa.gz 22-Mar-2014 15:22 10.5M [TXT] fish12.human.idtab 22-Mar-2014 17:23 1.6M [   ] fish12.human.names.gz 23-Mar-2014 02:13 856k [   ] fish12.kfish2.aa.gz 22-Mar-2014 15:22 13.3M [   ] fish12.kfish2.cds.gz 23-Mar-2014 01:58 21.5M [TXT] fish12.kfish2.idtab 23-Mar-2014 02:02 2.4M [   ] fish12.kfish2.names.gz 23-Mar-2014 02:13 1.0M [   ] fish12.mayzebr.aa.gz 22-Mar-2014 15:22 8.9M [   ] fish12.mayzebr.cds.gz 23-Mar-2014 01:52 16.1M [TXT] fish12.mayzebr.idtab 23-Mar-2014 01:50 1.4M [   ] fish12.mayzebr.names.gz 23-Mar-2014 02:13 499k [   ] fish12.medaka.aa.gz 22-Mar-2014 15:22 6.6M [   ] fish12.medaka.cds.gz 22-Mar-2014 17:43 10.9M [TXT] fish12.medaka.idtab 22-Mar-2014 17:23 1.5M [   ] fish12.medaka.names.gz 23-Mar-2014 02:13 270k [   ] fish12.platyfish.aa.gz 22-Mar-2014 15:22 7.5M [   ] fish12.platyfish.cds.gz 22-Mar-2014 17:43 12.4M [TXT] fish12.platyfish.idtab 22-Mar-2014 17:23 1.5M [   ] fish12.platyfish.names.gz 23-Mar-2014 02:13 264k [   ] fish12.spotgar3.aa.gz 22-Mar-2014 15:22 6.9M [   ] fish12.spotgar3.cds.gz 22-Mar-2014 17:43 11.3M [TXT] fish12.spotgar3.idtab 22-Mar-2014 17:23 1.4M [   ] fish12.spotgar3.names.gz 23-Mar-2014 02:13 256k [   ] fish12.stickleback.aa.gz 22-Mar-2014 15:22 7.0M [   ] fish12.stickleback.cds.gz 22-Mar-2014 17:43 11.7M [TXT] fish12.stickleback.idtab 22-Mar-2014 17:23 1.5M [   ] fish12.stickleback.names.gz 23-Mar-2014 02:13 295k [   ] fish12.tetraodon.aa.gz 22-Mar-2014 15:22 6.7M [   ] fish12.tetraodon.cds.gz 22-Mar-2014 17:43 11.0M [TXT] fish12.tetraodon.idtab 22-Mar-2014 17:23 1.4M [   ] fish12.tetraodon.names.gz 23-Mar-2014 02:13 298k [   ] fish12.tilapia.aa.gz 22-Mar-2014 15:22 8.0M [   ] fish12.tilapia.cds.gz 22-Mar-2014 17:43 13.4M [TXT] fish12.tilapia.idtab 22-Mar-2014 17:23 1.6M [   ] fish12.tilapia.names.gz 23-Mar-2014 02:13 289k [   ] fish12.zebrafish.aa.gz 22-Mar-2014 15:22 9.6M [   ] fish12.zebrafish.cds.gz 22-Mar-2014 17:43 15.7M [TXT] fish12.zebrafish.idtab 22-Mar-2014 17:23 1.9M [   ] fish12.zebrafish.names.gz 23-Mar-2014 02:13 429k


Developed at the Genome Informatics Lab of Indiana University Biology Department