Basic Local Alignment Search Tool* (BLASTn*/BLASTp*)
An algorithm for comparing primary biological sequence information.
BLAST*: Search for Biological Sequences
Performance Jumped by Up to 1.44x1
A BLAST* search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain similarity-score threshold.
BLAST is a cornerstone of many bioinformatics tool chains for sequencing genomic data. Industries that rely on this data are transforming rapidly, and the scalabilities of life sciences tool chains are not currently keeping pace with the enormous data growth provided by next-generation sequencing technology.
BLAST looks for similarities (homologs) in a nucleotide or protein query sequence of length n by aligning it against a subject sequence of length m. The NCBI BLAST* application suite supplies two flavors of DNA sequence match-searching applications: nucleotide-based (blastn*-type) and protein-based (blastp*-type).
BLASTn* Performance Results
The Intel® Xeon® processor E5-2697 v2 plus the Intel® Xeon Phi™ coprocessor 7120A are up to 1.44X faster than the Intel® Xeon® processor E5-2697 v2 baseline for BLASTn.
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BLASTp* Performance Results
The Intel® Xeon® processor E5-2697 v2 plus the Intel® Xeon Phi™ coprocessor 7120A are up to 1.25X faster than the Intel® Xeon® processor E5-2697 v2 baseline for BLASTp.
Genomics Codes
BWA-ALN* 0.5.10
A popular software package for mapping low-divergent sequences against a large-reference genome, such as the human genome.
MPI-HMMER* v2.3
An open-source implementation of the HMMER* protein sequence analysis suite.
BLASTn*/BLASTp*
An algorithm for comparing primary biological sequence information.
GATK*
A software package developed at the Broad Institute to analyze next-generation sequencing data.
QIAGEN
QIAGEN Bioinformatics* solutions deliver faster time to insight by combining powerful analytics that are able to interpret complex biological processes.
Halvade*
Halvade* is a MapReduce implementation of the best-practice DNA sequencing pipeline as recommended by Broad Institute.
ABySS*
ABySS* is an open-source de novo genome assembler for short paired-end reads.
DIDA*
DIDA* performs large-scale alignment tasks by distributing the indexing and alignment stages into smaller subtasks over a cluster of compute nodes.
elPrep*
elPrep* is a high-performance tool for preparing SAM/BAM/CRAM files for variant calling in genomic sequencing pipelines.
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Configuration Table
| System Overview | Intel® Xeon® Processor E5-2697 v2 with Intel® Xeon Phi™ Coprocessor 7120A |
|---|---|
| Platform | Intel® R2208GZ4GC platform, 2U chassis, hot-swap drives, 24 DIMMs, 1 750W redundant power supply |
| CPU/Stepping | Intel® Xeon® processor E5-2697 v2, 2.7 GHz , 12 core, 8 GT/s dual Intel® QuickPath Interconnect (Intel® QPI) links, 130W, 3.5 GHz max turbo frequency, 768 kB instr L1 / 3072 kB L2 / 30 MB L3 cache |
| Coprocessor | Intel® Xeon Phi™ coprocessor 7110 and 7120; 61 cores, 1.1 and 1.238 GHz, error-correcting code (ECC) enabled, Intel® Turbo Boost Technology disabled. |
| Software details | Intel® Manycore Platform Software Stack (Intel® MPSS) version — 2.1.6720-13/16/19, Flash* version — 2.1.03.0386 |
| Memory | Hynix HMT31GR7BFR-PB*, 64 GB total 8*8 GB 1600 MHZ Reg ECC DDR3 |
| Chipset | Rev 4.6, SE5C600.86B.99.99.x069.071520130923 |
| BIOS configuration | Default except: Intel® Turbo Boost Technology enabled, Enhanced Intel SpeedStep® Technology enabled, surface-mount technology (SMT) enabled, non-uniform memory access (NUMA) enabled, memory speed 1600 MHz, Note: all prefetchers enabled (this is default) |
| GigE node adapter | Intel® Ethernet Controller I350 (rev 01), 4 Gigabit network connections, only one connection in use |
| IB switch | 36-port switch/rack Mellanox FDR* (model MSX6025F-1BFR), Firmware version: 9_2_4002 |
| IB adapters | 36-port switch/rack Mellanox FDR (model MSX6025F-1BFR), Firmware version: 9_2_4002 |
| HDD specs | Seagate ST9600205SS* (scsi), 1x600 GB SAS HDD 10k RPM |
| Operating system | Red Hat Enterprise Linux* 6.4 |
Infos sur le produit et ses performances
1
Les résultats des bancs d'essai ont été obtenus avant le déploiement de récents correctifs logiciels et mises à jour micrologicielles destinés à faire face aux failles de sécurité « Spectre » et « Meltdown ». L'installation de ces mises à jour peut rendre ces résultats inapplicables à votre appareil ou système.
Les logiciels et charges de travail utilisés dans les tests de performance ont peut-être été optimisés uniquement pour les microprocesseurs Intel®. Les tests de performance tels que SYSmark* et MobileMark* portent sur des configurations, composants, logiciels, opérations et fonctions spécifiques. Les résultats peuvent varier en fonction de ces facteurs. Pour l'évaluation complète d'un produit, il convient de consulter d'autres tests et d'autres sources d'informations, notamment pour connaître le comportement de ce produit lorsqu'il est associé à d'autres composants. Consultez http://www.intel.fr/benchmarks à ce sujet.