Abstract:
BACKGROUND:Novel sequence motifs detection is becoming increasingly essential in computational biology. However, the high computational cost greatly constrains the efficiency of most motif discovery algorithms. RESULTS:In this paper, we accelerate MEME algorithm targeted on Intel Many Integrated Core (MIC) Architecture and present a parallel implementation of MEME called MIC-MEME base on hybrid CPU/MIC computing framework. Our method focuses on parallelizing the starting point searching method and improving iteration updating strategy of the algorithm. MIC-MEME has achieved significant speedups of 26.6 for ZOOPS model and 30.2 for OOPS model on average for the overall runtime when benchmarked on the experimental platform with two Xeon Phi 3120 coprocessors. CONCLUSIONS:Furthermore, MIC-MEME has been compared with state-of-arts methods and it shows good scalability with respect to dataset size and the number of MICs. Source code: https://github.com/hkwkevin28/MIC-MEME .
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Peng S,Cheng M,Huang K,Cui Y,Zhang Z,Guo R,Zhang X,Yang S,Liao X,Lu Y,Zou Q,Shi Bdoi
10.1186/s12859-018-2276-1subject
Has Abstractpub_date
2018-08-13 00:00:00pages
282issue
Suppl 9issn
1471-2105pii
10.1186/s12859-018-2276-1journal_volume
19pub_type
杂志文章abstract:BACKGROUND:Histopathology image analysis is a gold standard for cancer recognition and diagnosis. Automatic analysis of histopathology images can help pathologists diagnose tumor and cancer subtypes, alleviating the workload of pathologists. There are two basic types of tasks in digital histopathology image analysis: i...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1685-x
更新日期:2017-05-26 00:00:00
abstract:BACKGROUND:The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) in newly determined Poaceae trnL-F sequences and compare them with 533 previously determined sequences. It is supplied with input files design...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-173
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abstract:BACKGROUND:Complex networks are studied across many fields of science and are particularly important to understand biological processes. Motifs in networks are small connected sub-graphs that occur significantly in higher frequencies than in random networks. They have recently gathered much attention as a useful concep...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2009-10-04 00:00:00
abstract:BACKGROUND:Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determining systematically, which guide-trees, if any, give the best alignments. Some guide-tree constructi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-338
更新日期:2014-10-04 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2822-5
更新日期:2019-06-06 00:00:00
abstract:BACKGROUND:Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits. The traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression tra...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
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更新日期:2019-11-22 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
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更新日期:2005-02-23 00:00:00
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abstract:BACKGROUND:PSI-BLAST, an extremely popular tool for sequence similarity search, features the utilization of Position-Specific Scoring Matrix (PSSM) constructed from a multiple sequence alignment (MSA). PSSM allows the detection of more distant homologs than a general amino acid substitution matrix does. An accurate est...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2017-06-02 00:00:00
abstract:BACKGROUND:Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel methods including support vector machines, we propose stem kernels as an extension of string kernels for measuring the similarities between tw...
journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
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更新日期:2008-05-08 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2018-12-31 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2010-08-09 00:00:00
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abstract:BACKGROUND:Protein structure comparison is a fundamental task in structural biology. While the number of known protein structures has grown rapidly over the last decade, searching a large database of protein structures is still relatively slow using existing methods. There is a need for new techniques which can rapidly...
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journal_title:BMC bioinformatics
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