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)
-----

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
--------

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
#------------------