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Products > GenCore 6.0> Benchmarks


GenCore 6.0 Benchmarks:


Machine:
2 Quad Core Intel® Xeon® E5345, 2x4MB Cache, 2.33GHz, 1333MHz FSB, 4GB 667MHz (4x1GB) Dual Ranked DIMMs
OS: Red Hat Enterprise Linux Server, version 4, kernel 2.6.9-55.ELsmp 

Application
Query
Database
Time & speed
Smith&Waterman
hsactar
3,022 nt
est_human
3,219,654,488 nt
FASTA format
561 sec
34,687 MCPS
Smith&Waterman
bg044449
251 nt
est_human
3,219,654,488 nt
FASTA format
71 sec
22,764 MCPS

Smith&Waterman
hsactar
3,022 nt
patnt
1,440,902,433 nt
FASTA format
255 sec
34,152 MCPS
Smith&Waterman
bg044449
251 nt
patnt
1,440,902,433 nt
FASTA format
30 sec
24,111 MCPS




Smith&Waterman
acha_human
482 aa
uniprot
573,917,915 aa
FASTA format
19 sec
14,559 MCPS




tswp
bg044449
251 nt
uniprot
573,917,915 aa
FASTA format
30 sec
9,527 MCPS
tswn
acha_human
482 aa
patnt
1,440,902,433 nt
FASTA format
71 sec
19,563 MCPS




profilesearch
chap.prf
545 aa
uniprot
573,917,915 aa
FASTA format
45 sec
6,950 MCPS
tprofilesearch
chap.prf
545 aa
patnt
1,440,902,433 nt
FASTA format
225 sec
6,980 MCPS




frame+_n2p
bg044449
251 nt
uniprot
573,917,915 aa
FASTA format
127 sec
2,268 MCPS
frame+_p2n
acha_human
482 aa
patnt
1,440,902,433 nt
FASTA format
221 sec
6,285 MCPS




hmmer2search
pkinase
288 aa
uniprot
573,917,915 aa
FASTA format
61 sec
2,709 MCPS




hmmer2scan
acha_human
482 aa
Pfam_fs
1,711,961 aa
HMMER2 format
24 sec
34 MCPS
hmmer2scan
ryr1_rabit
5,037 aa
Pfam_fs
1,711,961 aa
HMMER2 format
25 sec
344 MCPS




gw9
pkinase
288 aa
gb_htg1
190,640,842 nt
FASTA format
1594 sec
68 MCPS
gw9scan
hsactar
3022 nt
Pfam_fs
1,711,961 aa
HMMER2 format
186 sec
111 MCPS

 

Name Description Sequences Bases
uniprot UniProt database version 4.2
ftp://ftp.uniprot.org/pub/databases/
uniprot/knowledgebase

1,803,406 573,917,915
pfam_fs The PFAM HMM library, local
alignment models ftp://ftp.genetics.wustl.edu/pub
/Pfam/Pfam_fs.gz

7,677
1,711,961
patnt An NCBI BLAST database:
patent nucleotide sequence database, directly from USPTO or from EU/Japan Patent Agencies via EMBL/DDBJ
ftp://ftp.ncbi.nlm.nih.gov/blast/db
/FASTA

2,436,366 1,440,902,433
est_human
An NCBI BLAST database: human est's
ftp://ftp.ncbi.nlm.nih.gov/blast/db
/FASTA

6,056,991
3,219,654,488
nt An NCBI BLAST database: nucleotide sequence database, with entries from all traditional divisions of GenBank, EMBL, and DDBJ excluding bulk divisions (gss,sts, pat, est, and htg divisions. wgs entries are also excluded. Not non-redundant.
ftp://ftp.ncbi.nlm.nih.gov/blast/db
/FASTA


3,111,972 14,000,712,433
htgs
An NCBI BLAST database: htgs database with entries from HTG division of GenBank, EMBL, and DDBJ
ftp://ftp.ncbi.nlm.nih.gov/blast/db
/FASTA

72,119
11,955,759,473
gb_htg1
one of the HTG files from gb144
1,330 190,640,842


Abbreviations:
nt - Nucleotides
aa - Amino Acids
MCPS - Million (Matrix) Cells Per Second