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Table 2 Percentage of genes detected using sequence alignment.

From: Gene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages

Reference Genome   Terminase Portal Head Tail Tape measure Prohead protease Lysin Holin Integrase
  E-value cutoff 0.01 0.1 0.01 0.1 0.01 0.1 0.01 0.1 0.01 0.1 0.01 0.1 0.01 0.1 0.01 0.1 0.01 0.1
Bacteriophage bIL285   31 37 33 50 - - 4 19 - - 46 49 16 18 11 23 57 64
Lactococcus phage TP901-1   8 22 13 19 12 27 7 22 96 98 - - 30 48 13 13 3 15
Enterobacteria phage HK97   29 40 35 43 4 26 12 19 83 96 54 64 0 4 5 24 54 73
Bacteriophage phi LC3   19 42 9 25 14 24 4 25 63 83 - - 36 48 13 14 58 65
Staphylococcus aureus phage phi 13   12 25 40 56 9 19 - - 77 94 36 38 - - 13 26 62 71
  1. The percentages are calculated by dividing the number of significantly similar sequences by the total number of sequences found by using regular expression. Sequence similarity is determined by BLAST (bl2seq) [33] using BLOSUM45 with indicated E-value cutoffs. Each sequence is "blasted" against its corresponding gene in the reference genome. The best cases are highlighted in bold.