Index of /EvidentialGene/plants/pine/refprot_align
Name Last modified Size
Parent Directory 20-Dec-2016 12:57 -
arath15ap-pine9set_aa.blasttab.gz 16-Dec-2016 20:50 5.2M
pine9set_refalign_stats.txt 20-Dec-2016 13:05 7k
vitvi15nc-pine9set_aa.blasttab.gz 16-Dec-2016 20:51 4.9M
Pine gene sets x Ref protein align stats
from blast hits table (blasttab = best 1 target source per ref prot)
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Reference gene sets:
arath15ap = Arabidopsis, Araport v2015
vitvi15nc = Vitis vin. grape, NCBI RefSeq genes v2015
Pine gene sets:
pitaeg8 = Evigene of 2 multi-kmer + trinity assemblies of Pinus taeda, 2013 august
eugenes.org/EvidentialGene/plants/pine/pine_evigene201308/publicset/
pitav1tr = old.evigene of 1 multi-kmer (Velvet/O), 2 trinity of Pinus taeda, 2013,
with ad-hoc removals (partial gene assemblies?)
pita2trpacbio = PacBio assemblies of Pinus taeda genes, 2016
pita1gmodl = Maker gene models of Pinus taeda, 2015? v1.1
treegenesdb.org/ftp/Genome_Data/genome/pinerefseq/Pita/
tsaGEUZ = Illumina-Trinty + PacBio assemblies of Pinus lamb. (pila, sugar pine), 2016, Genbank-TSA
pilav1gm = Maker gene models of Pinus lamb. (sugar), 2016
treegenesdb.org/ftp/Genome_Data/genome/pinerefseq/Pila/
tsaGECO = Evigene of 2 multi-kmer assemblies + trinity of Illumina of Pinus patula, 2015, GenBank-TSA
tsaGBLJ = Trinity of Illumina rnaseq of Pinus canariensis, 2015, GenBank-TSA
tsaGDQR = Trinity of Illumina rnaseq of Pinus albicaulis, 2015, GenBank-TSA
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Results of blastp -query ref.aa -db pine9set,
retabulated to bitscore, identity, align, query-len, source-len
.. by Don Gilbert, 2016.dec
Geneset Summary tables, ordered by pHit
arath15ap, mainref=1 nref=1 mieq=0.3
Geneset nHit pHit Algn Ident pAln pIden for nref=23161
pitaeg8 22652/23161 97.8 374.1 219.3 80.9 58.1
tsaGECO 22122/23161 95.5 375.6 220.3 80.4 57.8
tsaGBLJ 21322/23161 92 344.6 200 74.7 57.4
pita1gmodl 20741/23161 89.5 318 181.6 70.5 57
tsaGEUZ 20553/23161 88.7 351.7 207.1 75.3 58.3
pilav1gm 20275/23161 87.5 317.4 183.6 70.1 57.6
pitav1tr 19987/23161 86.2 332.8 188.8 70.8 55.9
pita2trpacbio 19792/23161 85.4 289.3 167.1 67.1 57
tsaGDQR 18830/23161 81.3 344.5 198.7 67.6 56.3
vitvi15nc, mainref=0 nref=1 mieq=0.3
Geneset nHit pHit Algn Ident pAln pIden for nref=35618
pitaeg8 35094/35618 98.5 428.2 250 82.7 58.6
tsaGECO 34530/35618 96.9 426.8 249.5 82.4 58.3
tsaGBLJ 33750/35618 94.7 393.5 227.8 77.1 57.8
tsaGEUZ 32152/35618 90.2 396.1 232.3 76.7 58.6
pita1gmodl 31837/35618 89.3 361.6 205.1 71 57.4
pitav1tr 31260/35618 87.7 380 214.5 72.7 56.1
pilav1gm 30981/35618 86.9 356.4 204.3 70 57.9
tsaGDQR 30200/35618 84.7 397.5 228.8 70.8 56.9
pita2trpacbio 30121/35618 84.5 314.2 182.1 66.7 57.6
#------------------
arath15ap, mainref=1 nref=1 mieq=0.3, longest 1000 REF
Geneset nHit pHit Algn Ident pAln pIden for nref=999
pitaeg8 994/999 99.4 1182.9 696.7 83.5 57.7
tsaGECO 980/999 98 1131.2 671.8 81.8 57.7
tsaGBLJ 971/999 97.1 997 585.7 72.5 57.3
tsaGDQR 963/999 96.3 1132.6 663 80.4 57
tsaGEUZ 909/999 90.9 1009.6 602.8 74 57.8
pitav1tr 866/999 86.6 971.5 556.8 70.3 55.6
pita1gmodl 830/999 83 860.5 493.5 63.2 56
pilav1gm 803/999 80.3 809.9 473.6 60 56.8
pita2trpacbio 742/999 74.2 591.1 346.3 46.4 57
#------------------
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