Dear arthropodists,
I'm in the process of building and testing a non-insect-centric arthropod
orthology gene set, that includes some transcript assembly for crustaceans
and ticks/Chelicerata. These I hope to make publicly available this spring.
They are from already published data but the protein genes are
hard to find for some, except the daphnia magna set is not yet
public. These will I think help to place genes of the rest of the
arthropods.
If you have comments/suggestions for this, let me know.
If in particular you know of public (or soon to be)
"complete" non-insect arthropod gene sets, clue me in.
A few of the transcript-data sets may be too poor to use (I get
only gene fragments, missing many orthologs), except maybe to
pick out a small subset of full genes. It appears currently that
the Chelicerata sets (now ixodes + spidermite, and very poor dog
tick assembly) are all artifactually incomplete, but the union of
these may provide a more complete Chelicerata orthology set.
- Don Gilbert
http://arthropods.eugenes.org/arthropods/orthologs/ARP3x/arpx_summary13d2.txt
======= orthomcl gene groups draft 2 ================
aax13u2omcl/Feb_18
Clade presence for gene families, ncommon gene=24565
Clade Only Miss OutAny OutOnly OutMiss
Crust 30 538 7033 165 183
Tick 61 1824 6272 48 566
inSect 300 3175 6533 114 324
----------------------------------------------
OutAny = 1+ species in clade has outgroup gene family;
OutOnly= 2+ species in clade have outgroup gene family, none of other clades have.
OutMiss= no species in clade has outgroup, both other clades have.
Only = all species in clade have family, none of other clades have
Miss = no species in clade has family, both other clades have
Outgroup set is human, zebrafish
Common gene families presence, ncommon=5416, min taxa=9
Species Have Miss
tribol 5223 193
daphmag 5202 214
wasp 5192 224
daphplx 5167 249
drosmel 5157 259
human 5110 306
zfish 5107 309
aphid 5051 365
ixodes 4777 639 # so-so incomplete geneset
tetur 4538 878 # so-so incomplete geneset
shrimp 4382 1034 # weak,incomplete gene set
barnacl 3466 1950 # very poor gene set
dogtick 2328 3088 # very poor gene set
-----------------------
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd from indiana.edu--http://marmot.bio.indiana.edu/