Académique Documents
Professionnel Documents
Culture Documents
see http://arthropods.eugenes.org/EvidentialGene/vertebrates/
TABLE GQ. Quality effect of gene set construction methods for vertebrate fish,
comparing methods NCBI Eukaryote annotation (nc), EvidentialGene (evg),
MAKER2 (mk), EvidenceModeller (em), within and across species.
Similar method quality rankings are obtained in gene sets of plants and arthropo
ds.
- Don Gilbert, 2016 Feb.
Highly conserved ortholog genes (BUSCO vertebrate set)
Expectation ~ 99% found, ~90% align, ~ <1% tiny or big extremes
Geneset
nGroup nFound %Found %Align %Tiny %Big
----------- ------------------------------------------------------kfish.evg
4097
4045 98.7 91.5 0.3 0.5
* high accuracy
kfish.nc
4097
4031 98.4 89.5 1.3 0.7
notfur.em
4097
3996 97.5 87.5 2.9 1.1
notfur.mk
4097
3726 90.9 76.6 5.2 2.2
- low accuracy
pike.nc
4097
4060 99.1 93.2 0.6 0.6
* high accuracy
pike.mk
4097
3114 76.0 56.5 7.8 0.2
- low accuracy
amolly.nc
4097
4050 98.9 92.2 0.8 0.8
* high accuracy
guppy.nc
4097
4048 98.8 91.5 0.8 1.0
* high accuracy
--------------------------------------------------------------------Ortholog groups common to 3+ reference fish
Expectation ~ 90% found, ~85% align, ~ 1-3% tiny or big extremes
Geneset
nGroup nFound %Found %Align %Tiny %Big
----------- ------------------------------------------------------kfish.evg
17904 16345 91.3
86.6 0.8 2.5 * high accuracy
kfish.nc
17904 15701 87.7
82.9 1.8 1.9
notfur.em
17904 15277 85.3
78.8 2.9 2.7
notfur.mk
17904 13706 76.6
67.4 5.8 6.9 - low accuracy
pike.nc
17904 15726 87.8
82.5 1.0 2.4
pike.mk
17904 11676 65.2
51.9 16.6 1.8 - low accuracy
amolly.nc
17904 15888 88.7
85.6 0.9 2.4 * high accuracy
guppy.nc
17904 15797 88.2
84.6 1.2 2.6 * high accuracy
zebrafish
17904 15050 84.1
77.6 2.4 1.3
--------------------------------------------------------------------Gene set method suffix: nc= NCBI Eukaryote annotation,
evg=EvidentialGene, mk= MAKER2, em = EvidenceModeller
Teleostei fish taxonomy tree
Euteleosteomorpha
+ Neoteleostei
+ + + + + + Haplochromini
+ + + + + + + Maylandia zebra
# mayzebr = african cichlid Zebra Mbuna
+ + + + + Cyprinodontiformes
+ + + + + + + Nothobranchius furzeri # notfur = african turquoise killifish
+ + + + + + + Poeciliidae
+ + + + + + + + + + Xiphophorus maculatus # platyfish
+ + + + + + + + + + Poecilia formosa
# amolly = amazon molly
+ + + + + + + + + + Poecilia reticulata # guppy
+ + + + + + + Fundulidae
+ + + + + + + + Fundulus heteroclitus # kfish = atlantic killifish
+ Protacanthopterygii
+ + Esox lucius
# northern pike
Otomorpha
+ + Cypriniphysae
+ + + Danio rerio
# Zebrafish
---------------------------------------------------------------------
1,456-520
25666-25782,21854-21918:-