|
GenCore 6.0 Benchmarks:
Machine:
2 õ 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
|
