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Table 2 Applied homology search strategies for ncRNAs

From: Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum

  Blast parameters  
Strategy -r -q -G -e -E -W TF
1 5 −4 10 NA 6 7 69 %
2 4 −5 3 NA 5 7 ?
3 5 −4 25 NA 10 7 69 %
4 4 −5 12 NA 8 7 ?
5(2) 4 −5 3 20 5 7 ?
6(3) 5 −4 25 20 10 7 69 %
7(2) 4 −5 3 1000 5 7 ?
8(3) 5 −4 25 1000 10 7 69 %
Default 1 -3 5 10 2 11 99 %
  1. -r: reward for a nucleotide match, -q: penalty for a nucleotide mismatch, -G: Cost to open a gap, -e: Expectation value, -E: Cost to extend a gap, -W: Word size. The Theoretical frequency (TF), is the expected frequency according to the established parameters [31]. The strategies 1, 2, 3 and 4 were suggested by [32], while the others were modifications of the strategies written parentheses, according to [31]. The ‘Default’ strategy represents the predetermined parameters for blastn program