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aligner_comparison.md

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Comparison with other aligners

Here are described results of speed comparison of OpAl with other aligners: SSW, SSEARCH(FASTA) and SWIPE.
SSW, SSEARCH and SWIPE do only Smith-Waterman alignment so we compared only for SW.

Aligners were tested by quering sequences against UniProtKB/Swiss-Prot database (contains 541762 sequences).
Database can be obtained from www.uniprot.org/downloads -> UniProtKB/Swiss-Prot.
Specific sequence can also be obtained from www.uniprot.org by searching it by name (Search tab).

All aligners were tested with following parameters:

  • number of threads = 1
  • gap opening = 3
  • gap extension = 1
  • score matrix = BLOSUM50

Only scores were calculated (not alignments). Time spent to read sequences and database was not measured.

How aligners were called:

  • SSW: ./ssw_test -p uniprot_sprot.fasta <query_file>
  • OpAl: ./opal_aligner -s <query_file> uniprot_sprot.fasta
  • SSEARCH: ./ssearch36 -d 0 -T 1 -p -f -3 -g -1 -s BL50 <query_file> uniprot_sprot.fasta
  • SWIPE: ./swipe -a 1 -p 1 -G 3 -E 1 -M BLOSUM50 -b 0 -i <query_file> -d uniprot_sprot NOTE: database had to be preprocessed for SWIPE using makeblastdb

Following table shows how much time took for different sequences to be aligned against UniProtKB/Swiss-Prot database. All times are in seconds. Test were performed on i7-4770K CPU @ 3.50GHz with 32GB RAM (AVX2 support).

O74807 P19930 Q3ZAI3 P18080
query length 110 195 390 513
SSW 9.0 16.6 25.8 31.0
OpAl(SSE4.1) 8.7 12.2 20.2 25.5
OpAl(AVX2) 5.2 6.9 10.8 14.7
SSEARCH 7.0 11.7 18.3 22.4
SWIPE 5.3 9.5 17.8 23.1