Index of /EvidentialGene/plants/corn/refprot_align
Name Last modified Size
Parent Directory 26-Jan-2017 21:02 -
arath15ap-fivecornsets_aa.blasttab.gz 26-Jan-2017 21:03 116M
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
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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
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