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Test Results

Page Contents

Four sample genomes were tested with MGEScan-LTR and MGEScan-nonLTR programs.

* Test genome sequences:
    1. melanogaster (dm3): ucsc
    1. intestinalis (KH): Ensembl
  • Test Environment:

    Cloud instances of FutureSystems at Indiana University (http://futuresystems.org).

  • Hardware Spec:
    • Intel Xeon X5550 2.66GHz
    • 8 vCPUs
    • 16 GB DDR3 1333 MHz
    • 160GB 7200RPM SATA
  • Operating System:
    • Ubuntu 14.04 LTS

Test Genome Sequences

image

D. melanogaster (dm3)

  • dm3.gff3 <sample/dm3.gff3.txt>
  • dm3.ltr.out <sample/dm3.ltr.out.txt>
  • dm3.en <sample/dm3.en.txt>
  • dm3.rt <sample/dm3.rt.txt>

Evaluation

Elapsed time for MGEScan (dm3)
Program Total nonLTR LTR Options
MGEScan1.3.1 3 hrs 40 mins (13,220 secs) 55 mins (3,320 secs) 2 hrs 45 mins (9,900 secs) HMMER2, no MPI
MGEScan2 2 hrs 35 mins (9,304 secs) 19 mins (1,170 secs) 2 hrs 35 mins (9,304 secs) HMMER3.1b1, no MPI
MGEScan2 with MPI 1 hr 48 mins (6,502 secs) 15 mins (929 secs) 1 hr 48 mins (6,502 secs) HMMER3.1b1, MPI with 4 processors

Extra Files

  • dm3.tar.gz <sample/dm3.tar.gz> (Compressed file)
  • en <sample/dm3/data/info/validation/en.txt>
  • rt <sample/dm3/data/info/validation/rt.txt>
  • R2.rt.pep <sample/dm3/data/info/full/R2/R2.rt.pep.txt>
  • R2.rt.dna <sample/dm3/data/info/full/R2/R2.rt.dna.txt>
  • R2.dna <sample/dm3/data/info/full/R2/R2.dna.txt>
  • R2.pep <sample/dm3/data/info/full/R2/R2.pep.txt>
  • I.en.dna <sample/dm3/data/info/full/I/I.en.dna.txt>
  • I.rt.dna <sample/dm3/data/info/full/I/I.rt.dna.txt>
  • I.en.pep <sample/dm3/data/info/full/I/I.en.pep.txt>
  • I.pep <sample/dm3/data/info/full/I/I.pep.txt>
  • I.dna <sample/dm3/data/info/full/I/I.dna.txt>
  • I.rt.pep <sample/dm3/data/info/full/I/I.rt.pep.txt>
  • Jockey.en.dna <sample/dm3/data/info/full/Jockey/Jockey.en.dna.txt>
  • Jockey.rt.pep <sample/dm3/data/info/full/Jockey/Jockey.rt.pep.txt>
  • Jockey.dna <sample/dm3/data/info/full/Jockey/Jockey.dna.txt>
  • Jockey.en.pep <sample/dm3/data/info/full/Jockey/Jockey.en.pep.txt>
  • Jockey.rt.dna <sample/dm3/data/info/full/Jockey/Jockey.rt.dna.txt>
  • Jockey.pep <sample/dm3/data/info/full/Jockey/Jockey.pep.txt>
  • R1.dna <sample/dm3/data/info/full/R1/R1.dna.txt>
  • R1.en.pep <sample/dm3/data/info/full/R1/R1.en.pep.txt>
  • R1.pep <sample/dm3/data/info/full/R1/R1.pep.txt>
  • R1.en.dna <sample/dm3/data/info/full/R1/R1.en.dna.txt>
  • R1.rt.dna <sample/dm3/data/info/full/R1/R1.rt.dna.txt>
  • R1.rt.pep <sample/dm3/data/info/full/R1/R1.rt.pep.txt>
  • CR1.en.dna <sample/dm3/data/info/full/CR1/CR1.en.dna.txt>
  • CR1.dna <sample/dm3/data/info/full/CR1/CR1.dna.txt>
  • CR1.pep <sample/dm3/data/info/full/CR1/CR1.pep.txt>
  • CR1.rt.pep <sample/dm3/data/info/full/CR1/CR1.rt.pep.txt>
  • CR1.rt.dna <sample/dm3/data/info/full/CR1/CR1.rt.dna.txt>
  • CR1.en.pep <sample/dm3/data/info/full/CR1/CR1.en.pep.txt>
  • nonltr.gff3 <sample/dm3/data/info/nonltr.gff3.txt>

C. intestinalis (KH)

  • KH.gff3 <sample/KH.gff3.txt>
  • KH.ltr.out <sample/KH.ltr.out.txt>
  • KH.en <sample/KH.en.txt>
  • KH.rt <sample/KH.rt.txt>

Evaluation

Elapsed time for C. intestinalis
Program Total nonLTR LTR Options
MGEScan1.3.1 5 hours 18 minutes 36 seconds 34 minutes 47 seconds 4 hours 43 minutes 49 seconds HMMER 2.3.2, no MPI
MGEScan2 4 hours 5 minutes 27 seconds 9 minutes 23 seconds 4 hours 5 minutes 27 seconds HMMER 3.1b1, no MPI
MGEScan2 with MPI 1 hour 22 minutes 37 seconds 3 minutes 2 seconds 1 hour 22 minutes 37 seconds HMMER 3.1b1, MPI with 4 processors

Extra Files

  • KH.tar.gz <sample/KH.tar.gz>

S. purpuratus (strPur2)

  • strPur2.gff3 <sample/strPur2.gff3.txt>
  • strPur2.ltr.out <sample/strPur2.ltr.out.txt>
  • strPur2.en <sample/strPur2.en.txt>
  • strPur2.rt <sample/strPur2.rt.txt>

Evaluation

Elapsed time for MGEScan (strPur2)
Program Total nonLTR LTR Options
MGEScan1.3.1 45 hrs 12 mins (162,723 secs) 6 hrs 34 mins (23,644 secs) 38 hrs 37 mins (139,079 secs) HMMER 2.3.2
MGEScan2 67 hrs 13 mins (242,002 secs) 7 hrs 53 mins (28,392 secs) 67 hrs 13 mins (242,002 secs) HMMER 3.1b1, no MPI
MGEScan2 with MPI 12 hrs 55 mins (46,550 secs) 2 hrs 36 mins (9,411 secs) 12 hrs 55 mins (46,550 secs) HMMER 3.1b1, MPI with 4 processors

Extra Files

  • strPur2.tar.gz <sample/strPur2.tar.gz>

D. pulex (GCA_000187875.1)

  • dpulex.gff3 <sample/dpulex.gff3.txt>
  • dpulex.ltr.out <sample/dpulex.ltr.out.txt>
  • dpulex.en <sample/dpulex.en.txt>
  • dpulex.rt <sample/dpulex.rt.txt>

Evaluation

Elapsed time for MGEScan (dpulex)
Program Total nonLTR LTR Options
MGEScan1.3.1 4 hrs 5mins (14,697 secs) 1hr 8mins (4,127 secs) 2 hrs 57 mins (10,570 secs) HMMER 2.3.2, no MPI
MGEScan2 2 hrs 36 mins (9,414 secs) 46 mins (2,780 secs) 2 hrs 36 mins (9,414 secs) HMMER 3.1b1, no MPI
MGEScan2 with MPI 1hr 3mins (3,823 secs) 15 mins (878 secs) 1 hr 3mins (3,823 secs) HMMER 3.1b1, MPI with 4 processors

Extra Files

  • dpulex.tar.gz <sample/dpulex.tar.gz>

Test Results with Previous MGEScan 1.3.1

    1. melanogaster: dmelanogaster.old.tar.gz <sample/old/dm3.old.tar.gz>
    1. pulex: dpulex.old.tar.gz <sample/old/dpulex.old.tar.gz>
    1. intestinalis: KH.old.tar.gz <sample/old/KH.old.tar.gz>
    1. purpuratus: strPur2.old.tar.gz <sample/old/strPur2.old.tar.gz>