Abstract:
BACKGROUND:Linkage disequilibrium (LD)-the non-random association of alleles at different loci-defines population-specific haplotypes which vary by genomic ancestry. Assessment of allelic frequencies and LD patterns from a variety of ancestral populations enables researchers to better understand population histories as well as improve genetic understanding of diseases in which risk varies by ethnicity. RESULTS:We created an interactive web module which allows for quick geographic visualization of linkage disequilibrium (LD) patterns between two user-specified germline variants across geographic populations included in the 1000 Genomes Project. Interactive maps and a downloadable, sortable summary table allow researchers to easily compute and compare allele frequencies and LD statistics of dbSNP catalogued variants. The geographic mapping of each SNP's allele frequencies by population as well as visualization of LD statistics allows the user to easily trace geographic allelic correlation patterns and examine population-specific differences. CONCLUSIONS:LDpop is a free and publicly available cross-platform web tool which can be accessed online at https://ldlink.nci.nih.gov/?tab=ldpop.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Alexander TA,Machiela MJdoi
10.1186/s12859-020-3340-1subject
Has Abstractpub_date
2020-01-10 00:00:00pages
14issue
1issn
1471-2105pii
10.1186/s12859-020-3340-1journal_volume
21pub_type
杂志文章abstract:BACKGROUND:Protein remote homology detection is one of the central problems in bioinformatics, which is important for both basic research and practical application. Currently, discriminative methods based on Support Vector Machines (SVMs) achieve the state-of-the-art performance. Exploring feature vectors incorporating...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2014-01-01 00:00:00
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journal_title:BMC bioinformatics
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abstract:BACKGROUND:Logic Learning Machine (LLM) is an innovative method of supervised analysis capable of constructing models based on simple and intelligible rules. In this investigation the performance of LLM in classifying patients with cancer was evaluated using a set of eight publicly available gene expression databases f...
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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更新日期:2011-10-05 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:2016-12-13 00:00:00
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journal_title:BMC bioinformatics
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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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journal_title:BMC bioinformatics
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更新日期:2016-01-16 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2017-02-02 00:00:00
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更新日期:2006-05-08 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:2016-10-03 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2012-01-01 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:2019-02-18 00:00:00
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更新日期:2016-08-30 00:00:00
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更新日期:2017-01-06 00:00:00
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pub_type: 杂志文章
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更新日期:2018-07-13 00:00:00
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pub_type: 杂志文章
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更新日期:2018-09-21 00:00:00
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更新日期:2015-09-15 00:00:00
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更新日期:2014-06-11 00:00:00
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更新日期:2006-05-04 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2018-06-18 00:00:00
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