Index of /EvidentialGene/plants/pine/pine_evigene201308/publicset

 Name                                     Last modified       Size  

 Parent Directory                         21-Feb-2021 23:12      -  
 evgTv1.aa_pub.fa.gz                      27-Aug-2013 13:12   175M  
 evgTv1.ann.txt.gz                        27-Aug-2013 13:09  29.3M  
 evgTv1.cds_pub.fa.gz                     27-Aug-2013 13:13   298M  
 evgTv1.mainalt.tab.gz                    27-Aug-2013 13:07   4.8M  
 evgTv1.mrna_pub.fa.gz                    27-Aug-2013 13:10   352M  
 evgTv1.pub.aa.qual                       25-Mar-2014 13:51  37.3M  
 evgTv1.pub_mainr.aa.qual                 26-Mar-2014 13:17   6.2M  
 evgTv1.realt.log                         27-Aug-2013 13:15     1k  
 evgTv1.realt_pubids.gz                   27-Aug-2013 13:15  20.2M  
 pine_evgTv1pub130827_iu14rna_ncbisra.txt 20-Feb-2021 21:23     5k  
 pine_evgTv1pub130827_main.aa.gz          26-Mar-2014 13:30  26.8M  
 pine_evgTv1pub130827_readme.txt          21-Feb-2021 23:10     2k  
 pinetv1reclass2.info                     27-Aug-2013 15:11    11k  

This Evigene reconstruction of Loblolly pine tree genes, of 2013 august, is
from of multi-kmer, 4 assemblers, Illumina RNA-seq, tagged "Pta.Tra13Evg" for Pinus taeda
associated with genome project  NCBI:PRJNA174450 of Pinus taeda (loblolly).

Source RNA-seq is at NCBI SRA, with SRA entries in pine_evgTv1pub130827_iu14rna_ncbisra.txt.

The gene sequences in evgTv1.mrna_pub.fa, with protein evgTv1.aa_pub.fa and CDS evgTv1.cds_pub.fa
contain a super-set of final gene transcripts: 458487 final kept set, and 413485 dropped as redundant (alternates).
The table of gene/transcript IDs and class, is in evgTv1.realt_pubids, with "drop" indicating discards.
Annotation table evgTv1.ann.txt includes protein name, size and homology database IDs. 
The subset of primary (longest), kept proteins per gene loduc is in pine_evgTv1pub130827_main.aa

Further statistics are in pinetv1reclass2.info including this summary of classes kept and dropped:
publicset3/evgTv1.realt_pubids
         Keep                Drop
  105310 althi         33299 dropalthi
  171593 althi1       165542 dropalthi1
   53546 altmid        34990 dropaltmid
    2849 altmida2       1299 dropaltmida2
   15835 altmidfrag    60080 dropaltmidfrag
     392 altmidfraga2   4552 dropaltmidfraga2
   77124 main              0
    5874 maina2            0
   62242 noclass       76801 dropnoclass
     581 noclassa2        62 dropnoclassa2
  ---------------------------------------
  495346 total        376625 droptotal 
  177982 aaref         44855 aaref
    49%, 71228/146480   of loci have TAIR/CDD aaref

where locus primary transcripts are "main", "maina2", noclass and noclassa2 (noclass = no alternates,
main = has alternates, a2 = protein duplicate, ie paralog). "aaref" have measured protein homology.