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Table 1 The percentages of all three cases of paired-end read alignments by HMMER and Short-Pair for the Arabidopsis RNA-Seq dataset

From: A sensitive short read homology search tool for paired-end read sequencing data

Case

HMMER,

HMMER,

HMMER,

Short-Pair

 

E-value 10

w/o filtration,

GA cutoff

 
  

E-value 10

  

Case 1

34.51%

32.83%

22.51%

0.42%

Case 2

28.42%

31.58%

8.84%

62.51%

Case 3

37.07%

35.59%

68.65%

37.07%

  1. “HMMER w/o filtration” : running HMMER by turning off all filtration steps. “HMMER GA cutoff”: applying HMMER with gathering thresholds