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Index of /EvidentialGene/plants/corn/refprot_align

      Name                                  Last modified       Size  

[DIR] Parent Directory 26-Jan-2017 21:02 - [   ] arath15ap-fivecornsets_aa.blasttab.gz 26-Jan-2017 21:03 116M [TXT] cornfivesets_refalign_stats.txt 26-Jan-2017 21:45 2k [   ] sorghum-fivecornsets_aa.blasttab.gz 26-Jan-2017 21:07 110M


Corn five gene sets Protein Homology evaluation
Results of blastp -db fivecornsets -query refplant.aa
tabulated to bitscore, identity, align, query-len, source-len
.. by Don Gilbert, 2016.dec

Reference proteins
 arath15ap = Arabidopsis, Araport 2015
 refSbicolor_313 = Sorghum, JGI/Phytozome 2016

Maze Gene sets
EVm5fZm = EvidentialGene 2016-Oct, gene assembly of Illumina RNA
Ens6Zm = Ensembl/Gramene gene models of 2016-Sep (Maize V4 chr)
Csh6pb = CSHL/Gramene PacBio gene assemblies of RNA, 2016-Jun (on Maize V4 chr)
Ncb3Zm = NCBI Refgen V3 (2014?) gene models
Jgi4Zm = JGI Rannotator gene assembly of Illumina RNA, 2014

Protein sets, longest 1000 protein  size stats
EVm5fZm nt=231177; average=2129; median=1953; min,max=1651,5425; nfull=937; 
Ens6Zm  nt=149669; average=2326; median=2208; min,max=2024,5267; nfull=; 
Csh6pb  nt=375085; average=2205; median=2149; min,max=1964,3100; nfull=967; 
Ncb3Zm  nt=58277;  average=1686; median=1527; min,max=1252,5104; nfull=; 
Jgi4Zm  nt=187045; average=1484; median=1330; min,max=1094,5425; nfull=940; 

Summary alignment stats for maize gene sets to reference primary isoforms

refSbicolor_313
Source	nHit	pAln	Iden	Algn	Rlen	Qlen	IdenH	AlgnH, nref=29023
EVm5fZ	28549	92.8	356.3	424	434.8	473.6	362.3	431
Ens6Zm	28144	91	346.4	408.7	437.4	466.7	357.3	421.5
Ncb3Zm	27963	90.3	339	404.7	440.3	464.1	351.8	420
Csh6pb	27007	84.2	310.4	385.7	447	461.5	333.6	414.5
Jgi4Zm	26932	83	310.3	382.8	450	462.6	334.4	412.5

arath15_aport20150701
Source	nHit	pAln	Iden	Algn	Rlen	Qlen	IdenH	AlgnH, nref=23579
EVm5fZ	23301	89.4	255.4	415.9	444.7	500.9	258.5	420.9
Ens6Zm	23254	87.6	244.2	403.8	446.7	491	247.6	409.4
Ncb3Zm	23271	87	237	396.2	446.7	487.2	240.2	401.4
Csh6pb	22822	84.2	231.1	388.2	449.9	479.8	238.8	401.1
Jgi4Zm	22614	83.3	230	385.9	452.5	491.1	239.8	402.3
---------------
Stats: 
 nHit = number ref proteins found (signif. blastp align, evalue <= 1e-5)
 pAlgn = ave percent align to reference, 
 Iden, Algn = ave. identity align, total align to ref proteins, all nref
 IdenH, AlgnH = ave. identity align, total align to ref proteins, nHit relative
 Rlen, Qlen = ave. amino length for reference, query (corn) proteins


Developed at the Genome Informatics Lab of Indiana University Biology Department