GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array
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{"title"=>"GHOSTX: An improved sequence homology search algorithm using a query suffix array and a database suffix array", "type"=>"journal", "authors"=>[{"first_name"=>"Shuji", "last_name"=>"Suzuki", "scopus_author_id"=>"55732170100"}, {"first_name"=>"Masanori", "last_name"=>"Kakuta", "scopus_author_id"=>"36625439000"}, {"first_name"=>"Takashi", "last_name"=>"Ishida", "scopus_author_id"=>"56421133100"}, {"first_name"=>"Yutaka", "last_name"=>"Akiyama", "scopus_author_id"=>"7202114141"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84905455179", "sgr"=>"84905455179", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0103833", "pmid"=>"25099887", "pui"=>"373700851"}, "id"=>"b79bca76-0245-316d-9698-49e3f05b0274", "abstract"=>"DNA sequences are translated into protein coding sequences and then further assigned to protein families in metagenomic analyses, because of the need for sensitivity. However, huge amounts of sequence data create the problem that even general homology search analyses using BLASTX become difficult in terms of computational cost. We designed a new homology search algorithm that finds seed sequences based on the suffix arrays of a query and a database, and have implemented it as GHOSTX. GHOSTX achieved approximately 131-165 times acceleration over a BLASTX search at similar levels of sensitivity. GHOSTX is distributed under the BSD 2-clause license and is available for download at http://www.bi.cs.titech.ac.jp/ghostx/. Currently, sequencing technology continues to improve, and sequencers are increasingly producing larger and larger quantities of data. This explosion of sequence data makes computational analysis with contemporary tools more difficult. We offer this tool as a potential solution to this problem.", "link"=>"http://www.mendeley.com/research/ghostx-improved-sequence-homology-search-algorithm-using-query-suffix-array-database-suffix-array", "reader_count"=>55, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>5, "Student > Master"=>15, "Other"=>2, "Student > Bachelor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>5, "Student > Master"=>15, "Other"=>2, "Student > Bachelor"=>5}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>12, "Mathematics"=>1, "Agricultural and Biological Sciences"=>24, "Medicine and Dentistry"=>1, "Computer Science"=>12}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>24}, "Computer Science"=>{"Computer Science"=>12}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>2, "United Kingdom"=>1, "Spain"=>1}, "group_count"=>2}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1623105"], "description"=>"<div><p>DNA sequences are translated into protein coding sequences and then further assigned to protein families in metagenomic analyses, because of the need for sensitivity. However, huge amounts of sequence data create the problem that even general homology search analyses using BLASTX become difficult in terms of computational cost. We designed a new homology search algorithm that finds seed sequences based on the suffix arrays of a query and a database, and have implemented it as GHOSTX. GHOSTX achieved approximately 131–165 times acceleration over a BLASTX search at similar levels of sensitivity. GHOSTX is distributed under the BSD 2-clause license and is available for download at <a href=\"http://www.bi.cs.titech.ac.jp/ghostx/\" target=\"_blank\">http://www.bi.cs.titech.ac.jp/ghostx/</a>. Currently, sequencing technology continues to improve, and sequencers are increasingly producing larger and larger quantities of data. This explosion of sequence data makes computational analysis with contemporary tools more difficult. We offer this tool as a potential solution to this problem.</p></div>", "links"=>[], "tags"=>["genetics", "genomics", "metagenomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "sequence alignment", "Database and informatics methods", "Database searching", "homology", "algorithm", "query", "suffix"], "article_id"=>1128975, "categories"=>["Biological Sciences"], "users"=>["Shuji Suzuki", "Masanori Kakuta", "Takashi Ishida", "Yutaka Akiyama"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0103833", "stats"=>{"downloads"=>8, "page_views"=>32, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GHOSTX_An_Improved_Sequence_Homology_Search_Algorithm_Using_a_Query_Suffix_Array_and_a_Database_Suffix_Array_/1128975", "title"=>"GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-06 02:44:02"}

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Relative Metric

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