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Table 2 Summary of transcriptome analysesa

From: Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses

Transcriptome analyses W5 cDNA
Roche 454 GS FLX  
Run cycles
Total number of reads
Total read length, Mb
   Average read length, bp 210.2
Illumina GA II Paired-End  
   Read length, bp 40 + 40
   Run lanes 1
Total number of reads
Total read length, Mb
   GC content 37.1%
Contig assembly  
   Contig numbers 20,232
   Total contig lengths, Mb 9.0
   Average contig length, bp 447.2
   Largest contig length, bp 4,397
Gene prediction, length > 500 bp  
   Number of ORFs 2,284
   Number of domains predicted in ORFs 9,720
   Average ORF length, bp 846.9
   Maximum RPKMb value 31,647.2
   Number of GH-like contigs 219
  1. aGC: the nucleotide G+C % ; GH: glycosyl hydrolase; ORF: open reading frame; RPKM: Reads Per Kilobase of exon model per Million mapped reads. bRPKM is a method for estimating relative expression levels of a transcriptome by normalizing short-read expressed tags from deep sequencing over ORF length and total reads (RPKM) [35].