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Index of /EvidentialGene/arthropods/daphnia/DaphniaSpecies17Orthology/daph10_omcl

      Name                                 Last modified       Size  

[DIR] Parent Directory 11-Dec-2017 13:37 - [TXT] EvigeneOrthoMCLMethods.txt 29-Nov-2017 15:22 2k [   ] all_orthomcl.out.gz 14-Nov-2017 13:48 1.1M [TXT] 14-Nov-2017 13:51 1k [TXT] 14-Nov-2017 13:51 1k [TXT] 14-Nov-2017 13:51 47k [TXT] 14-Nov-2017 13:50 921k [TXT] 14-Nov-2017 13:50 1k [TXT] 14-Nov-2017 13:50 1k [TXT] daph10omcla.aa.qual 13-Nov-2017 11:31 19.8M [   ] daph10omcla.bpo.gz 14-Nov-2017 08:37 341M [   ] 14-Nov-2017 08:23 775k [TXT] 14-Nov-2017 14:18 14.8M [TXT] 14-Nov-2017 14:15 16.7M [   ] daph10omcla_genes.ugp.txt.gz 15-Nov-2017 15:25 5.5M [   ] daph10omcla_genes.ugp.xml 15-Nov-2017 15:48 49.1M [TXT] daph10omcla_genes.ugp_brief.txt 15-Nov-2017 15:25 6.4M [TXT] daph10omcla_omclgn.consensus_def.txt 15-Nov-2017 15:25 2.3M [TXT] 14-Nov-2017 13:48 6.4M [TXT] 14-Nov-2017 13:50 14.9M [   ] 14-Nov-2017 13:50 41.6M [TXT] daph10omcla_omsubgrp1.list 14-Nov-2017 13:51 382k [TXT] daph10omcla_omsubgrp1.names 15-Nov-2017 15:26 254k [TXT] orthomcl.log 14-Nov-2017 09:00 113k [TXT] parameter.log 14-Nov-2017 09:00 2k [   ] 08-Nov-2017 21:50 2k [   ] 14-Nov-2017 13:46 1k [   ] 15-Nov-2017 14:19 3k [   ] 15-Nov-2017 15:47 3k

Evigene Methods for Orthology Assessment
for daph10_omcl gene clustering of Daphnia, Insects and Fishes (+human)

Method Steps: 
1.  collect species gene proteins, primary isoform only, for 10 species, in daph10omcl.aa
    each header has species tag:ID prefix.  Extract gene Names from aa headers for use below.
2.  blastp -db daph10omcl.aa -query daph10omcl.aa -evalue 1e-5 -outfmt 7 -out daph10omcl.aa.blastp
3.  tabulate daph10omcl.aa.blastp and run OrthoMCL (Evigene repackage), using MCL Markov clustering script
4.  outputs: daph10omcla.bpo,.gg are intermediate inputs to, 
    all_orthomcl.out and tmp/ files are cluster outputs.
5.  tabulate orthomcl.out to summary tables and annotated gene groups, with input gene.names (from aa headers) script
6.  summary and gene group outputs:
    intermediate tables are (OMCL group per gene), (pairwise genes per omcl group), shorter of daph10omcla_omclgns2. table of species presence/gene count per group, : brief summaries per species of group types (orlog,parlog,..), table of 1:1 ortholog species presence (from and or1inpar-count tab, species matrix of ortholog counts shared by species pairs,
	orsinpar = all orthologs, or1inpar = closest ortholog (orlog1) only.  Matrix diagonal is paralog count
        per species, : per species table of ortholog, paralog
       pairings, from that has all species
    daph10omcla_genes.ugp.txt, daph10omcla_genes.ugp.xml : annotated gene groups, with consensus group name,
       counts, and per-species genes listed
    daph10omcla_genes.ugp_brief.txt : from ugp.txt, stripping long list of species genes (one line/group)

Developed at the Genome Informatics Lab of Indiana University Biology Department