Basic Local Alignment Search Tool* (BLASTn*/BLASTp*)

An algorithm for comparing primary biological sequence information.

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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Reproduce these results with this optimization recipe ›

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.

Download the code ›

Reproduce these results with this optimization recipe ›

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

Product and Performance Information

1

Benchmark results were obtained prior to implementation of recent software patches and firmware updates intended to address exploits referred to as "Spectre" and "Meltdown". Implementation of these updates may make these results inapplicable to your device or system.

Software and workloads used in performance tests may have been optimized for performance only on Intel® microprocessors. Performance tests, such as SYSmark* and MobileMark*, are measured using specific computer systems, components, software, operations and functions. Any change to any of those factors may cause the results to vary. You should consult other information and performance tests to assist you in fully evaluating your contemplated purchases, including the performance of that product when combined with other products. For more complete information visit https://www.intel.com/benchmarks.

Intel is a sponsor and member of the BenchmarkXPRT Development Community, and was the major developer of the XPRT family of benchmarks. Principled Technologies is the publisher of the XPRT family of benchmarks.