Skip to main content

Table 4 The integration of ANN and BLAST (IAB algorithm).

From: Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis

IABa (T,N,F)b
1. size ← length [T ] - N
2. Oligo allOligo [size]/* the data structure Oligo includes score and sequence*/
3. for pos ← 1 to size
4. do allOligo [pos].sequenceT.substring (pos, pos + N)
5. /* calculate the ANN score for each sliding oligo using the trained ANN */
6. allOligo [pos].score = CalScoreByNN c (allOligo [pos ])
7. sort the allOligo array into non-decreasing order by ANN score
8. lowestSim ← 1.0
9. for p ← 0 to(sizeFd)
10. do oligoallOligo [p].sequence
11. similarity ← CalSimByBlast e (oligo)
12. if similarity < lowestSim
13. then bestOligooligo
14. lowestSimsimilarity
15. if lowestSim <TH sim f
16. then return bestOligo
17. return bestOligo
  1. aIAB, integration of artificial neural network (ANN) and basic local alignment search tool (BLAST). bThe input parameters are as follows: the THC sequence T, the oligo length N, and the sensitivity factor F; cCalScoreByNN procedure calculates the ANN score (indicates the cross homology) by trained ANN; dThe sensitivity factor is set as 0.2, 0.3, and 0.4; eCalSimByBlast procedure calculates the cross homology by WU-BLAST; fThe cross homology threshold (TH sim ) used for 70-mer and 50-mer was 0.7 and that used for 25-mer was 0.8.