Flak 1.0 - Ultra-fast Fuzzy Whole-genome Alignment
Flak 1.0 - Ultra-fast Fuzzy Whole-genome Alignment   Download FLAK 1.0

 

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Performance Benchmarks

FLAK has been extensively tested and benchmarked against alternative genome alignment systems. The times and memory requirements for whole genome alignments, in both forward and reverse orientations, over an indicative range of different organisms are listed below. For these benchmarks, FLAK was configured with the 13/20 spaced-seed ####-#--##--##-#-### and a β-Cutoff Threshold of 0.8. The alignments were executed on a LinuxMint 17.0.1 platform, with a 2.4 GHz Intel Core i7 processor and 16GB of RAM. In addition, an instance of the Java HotSpot 1.8 64-bit virtual machine was used as the runtime environment to test FLAK.

 

Bacterial Genomes

Query SequenceQuery Size (Mbps)Reference SequenceReference Size (Mbps)Time (secs)
Brucella suis 13302.1Brucella suis ATCC 234451.91
Chlamydophila pneumoniae CWL0291.2Chlamydophila pneumoniae J1381.2< 1
Clostridium botulinum A34.0Clostridium perfringens ATCC 131243.33
Corynebacterium urealyticum DSM 71092.4Corynebacterium glutamicum ATCC 130323.31
Escherichia coli K-12 MG16554.7Escherichia coli 5365.03
Haemophilus influenzae F30312.0Haemophilus influenzae F30472.01
Helicobacter pylori 20171.5Helicobacter pylori F161.51
Kebsiella pneumoniae MGH 785785.3Escherichia coli K-12 MG16554.73
Neisseria meningitidis 80132.3Neisseria meningitidis FA10902.11
Rickettsia typhi1.1Rickettsia prowazekii1.1< 1
Salmonella enterica serovar typhimurium LT24.9Escherichia coli K-12 MG16554.73
Shewanella oneidensis MR 15.0Shewanella sp. ANA 35.03
Shigella boydii4.5Shigella flexneri4.64
Sinorhizobium meliloti 10213.7Sinorhizobium fredii HH1034.32
Staphylococcus aureus COL2.8Staphylococcus aureus JH1 2.92
Synechococcus sp. WH81092.1synechococcus sp. CC96052.51
Yersinia pestis CO924.7Yersinia pestis KIM4.63
Parameters: Minimum match length = 32, Repeat filter off, Clustering off.

 

Simple Eukaryotes - Yeasts, Protozoans and Fungi

Query SequenceQuery Size (Mbps)Reference SequenceReference Size (Mbps)Time (secs)
Saccharomyces cerevisiae12.2Schizosaccharomyces pombe12.810
Plasmodium falciparum 3D723.6Plasmodium yoelii22.463
Aspergillus fumigatus29.8Aspergillus nidulans30.125
Parameters: Minimum match length = 64, Repeat filter on, Clustering off.

 

Flies - Drosophila

Query SequenceQuery Size (Mbps)Reference SequenceReference Size (Mbps)Time (secs)
Drosophila simulans Muller Elements A-F119.9Drosophila melanogaster Muller Elements A-F122.1155
Drosophila yakuba Muller Elements A, B/C, C/B, D, E, F121.3Drosophila melanogaster Muller Elements A-F122.1153
Drosophila miranda138.7Drosophila melanogaster Muller Elements A-F122.1154
Parameters: Minimum match length = 64, Repeat filter on, Clustering off.

 

Mammals (Chromosome Comparisons)

Query SequenceQuery Size (Mbps)Reference SequenceReference Size (Mbps)Time (secs)
Homo sapiens Chr X158.3Mus musculus Chr X169.3189
Parameters: Minimum match length = 64, Repeat filter on, Clustering off.

 

 

 

© 2016.  FLAK (Fuzzy Logic Analysis of k-mers) Version 1.0     
Flak 1.0 - Ultra-fast Fuzzy Whole-genome Alignment