SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification
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{"title"=>"SECOM: A novel hash seed and community detection based-approach for genome-scale protein domain identification", "type"=>"journal", "authors"=>[{"first_name"=>"Ming", "last_name"=>"Fan", "scopus_author_id"=>"57197071766"}, {"first_name"=>"Ka Chun", "last_name"=>"Wong", "scopus_author_id"=>"35241044600"}, {"first_name"=>"Taewoo", "last_name"=>"Ryu", "scopus_author_id"=>"16508181500"}, {"first_name"=>"Timothy", "last_name"=>"Ravasi", "scopus_author_id"=>"6603069555"}, {"first_name"=>"Xin", "last_name"=>"Gao", "scopus_author_id"=>"55712115900"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22761802", "doi"=>"10.1371/journal.pone.0039475", "pui"=>"365122159", "issn"=>"19326203", "sgr"=>"84862996847", "scopus"=>"2-s2.0-84862996847"}, "id"=>"fd2a1be6-e0d8-3c1e-8e72-6c3722c029bd", "abstract"=>"With rapid advances in the development of DNA sequencing technologies, a plethora of high-throughput genome and proteome data from a diverse spectrum of organisms have been generated. The functional annotation and evolutionary history of proteins are usually inferred from domains predicted from the genome sequences. Traditional database-based domain prediction methods cannot identify novel domains, however, and alignment-based methods, which look for recurring segments in the proteome, are computationally demanding. Here, we propose a novel genome-wide domain prediction method, SECOM. Instead of conducting all-against-all sequence alignment, SECOM first indexes all the proteins in the genome by using a hash seed function. Local similarity can thus be detected and encoded into a graph structure, in which each node represents a protein sequence and each edge weight represents the shared hash seeds between the two nodes. SECOM then formulates the domain prediction problem as an overlapping community-finding problem in this graph. A backward graph percolation algorithm that efficiently identifies the domains is proposed. We tested SECOM on five recently sequenced genomes of aquatic animals. Our tests demonstrated that SECOM was able to identify most of the known domains identified by InterProScan. When compared with the alignment-based method, SECOM showed higher sensitivity in detecting putative novel domains, while it was also three orders of magnitude faster. For example, SECOM was able to predict a novel sponge-specific domain in nucleoside-triphosphatase (NTPases). Furthermore, SECOM discovered two novel domains, likely of bacterial origin, that are taxonomically restricted to sea anemone and hydra. SECOM is an open-source program and available at http://sfb.kaust.edu.sa/Pages/Software.aspx.", "link"=>"http://www.mendeley.com/research/secom-novel-hash-seed-community-detection-basedapproach-genomescale-protein-domain-identification", "reader_count"=>9, "reader_count_by_academic_status"=>{"Researcher"=>3, "Student > Ph. D. Student"=>2, "Student > Bachelor"=>1, "Professor"=>2, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Researcher"=>3, "Student > Ph. D. Student"=>2, "Student > Bachelor"=>1, "Professor"=>2, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Agricultural and Biological Sciences"=>4, "Social Sciences"=>1, "Computer Science"=>2, "Unspecified"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Computer Science"=>{"Computer Science"=>2}, "Environmental Science"=>{"Environmental Science"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Saudi Arabia"=>1, "United States"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/616912"], "description"=>"<p>The distribution of the clusters with larger sizes, containing at least 11 segments, are enlarged as the inset.</p>", "links"=>[], "tags"=>["sizes", "segments"], "article_id"=>287405, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Ming Fan", "Ka-Chun Wong", "Taewoo Ryu", "Timothy Ravasi", "Xin Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039475.g003", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_cluster_sizes_for_the_domain_segments_predicted_by_SECOM_/287405", "title"=>"Distribution of cluster sizes for the domain segments predicted by SECOM.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-28 02:03:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/616831"], "description"=>"<p>SECOM and DIVCLUS are first tested by recovering the Pfam and Superfamily domains annotated by InterProScan. The putative novel domains predicted by SECOM and DIVCLUS are then compared against each other. The putative novel domains predicted only by SECOM are finally analyzed.</p>", "links"=>[], "tags"=>["multi-step", "validation"], "article_id"=>287326, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Ming Fan", "Ka-Chun Wong", "Taewoo Ryu", "Timothy Ravasi", "Xin Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039475.g002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_the_multi_step_validation_procedure_to_evaluate_the_performance_of_SECOM_/287326", "title"=>"Illustration of the multi-step validation procedure to evaluate the performance of SECOM.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-28 02:02:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/617123"], "description"=>"<p>PSIPRED <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039475#pone.0039475-Jones1\" target=\"_blank\">[8]</a> is used to predict the secondary structures of the consensus sequences of the three domains. CON stands for the consensus sequences and SS stands for the predicted secondary structures. (A). ClustalX alignment of the 19 segments. The protein IDs are those of the best BLAST hit in <i>A. queenslandica</i> followed by the location of the predicted domain. The hash seeds that correspond to the communities from which the cluster is built are boxed. (B) and (C). ClustalX alignments of two putative novel domains predicted by SECOM only. NV stands for sea anemone and HM stands for hydra.</p>", "links"=>[], "tags"=>["putative", "domains", "secom"], "article_id"=>287611, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Ming Fan", "Ka-Chun Wong", "Taewoo Ryu", "Timothy Ravasi", "Xin Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039475.g005", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Three_putative_novel_domains_predicted_by_SECOM_only_/287611", "title"=>"Three putative novel domains predicted by SECOM only.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-28 02:06:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/617332"], "description"=>"<p>The first column lists the size of the clusters. The second column lists the number of protein sequences that have at least one annotated Pfam or Superfamily domain. The third and fourth columns list the most frequent annotated domains and their frequencies in the clusters. The fifth column shows the domain descriptions. The sixth column lists the enriched Gene Ontology (GO) function (if available).</p>", "links"=>[], "tags"=>["annotated", "domains", "10", "largest", "clusters", "secom", "covered", "interproscan"], "article_id"=>287815, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Ming Fan", "Ka-Chun Wong", "Taewoo Ryu", "Timothy Ravasi", "Xin Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039475.t003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_shared_annotated_domains_of_the_10_largest_clusters_detected_by_SECOM_but_not_covered_by_InterProScan_or_DIVCLUS_/287815", "title"=>"Summary of shared annotated domains of the 10 largest clusters detected by SECOM but not covered by InterProScan or DIVCLUS.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-28 02:10:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/616996"], "description"=>"<p>(A)–(E). ROC curves for SECOM (magenta) and DIVCLUS (cyan) on sponge, coral, hydra, urchin and sea anemone, respectively. (F). Precision-recall curves for SECOM (magenta) and DIVCLUS (cyan) on sponge. The ROC plots suggest that SECOM provides a better overall performance. At small false positive rate, SECOM has very similar but slightly lower AUC, i.e., AUC for FPR below 5% is 0.0056 v.s. 0.0064, 0.0022 v.s. 0.0025, 0.0016 v.s. 0.0020, 0.0062 v.s. 0.0062, and 0.0017 v.s. 0.0150 on sponge, coral, hydra, urchin and sea anemone, respectively.</p>", "links"=>[], "tags"=>["varying"], "article_id"=>287490, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Ming Fan", "Ka-Chun Wong", "Taewoo Ryu", "Timothy Ravasi", "Xin Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039475.g004", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_with_varying_thresholds_/287490", "title"=>"Performance with varying thresholds.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-28 02:04:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/616739"], "description"=>"<p>Given a set of protein sequences (“A” to “H”), SECOM first finds all the hash seeds (“1” to “9”) that appear at least twice in this set. A seed-protein graph is then built, in which each node is a protein sequence and two nodes are connected if they share at least one hash seed. The highly connected subgraphs (i.e., communities) are found in this graph. The communities can be overlapping and each of them (“Domain I” and “Domain II”) is a predicted domain cluster by SECOM.</p>", "links"=>[], "tags"=>["Computational biology", "biophysics", "Biochemistry"], "article_id"=>287228, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Ming Fan", "Ka-Chun Wong", "Taewoo Ryu", "Timothy Ravasi", "Xin Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039475.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Outline_of_SECOM_/287228", "title"=>"Outline of SECOM.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-28 02:00:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/321107", "https://ndownloader.figshare.com/files/321152", "https://ndownloader.figshare.com/files/321185", "https://ndownloader.figshare.com/files/321216", "https://ndownloader.figshare.com/files/321252", "https://ndownloader.figshare.com/files/321286", "https://ndownloader.figshare.com/files/321327", "https://ndownloader.figshare.com/files/321365", "https://ndownloader.figshare.com/files/321400", "https://ndownloader.figshare.com/files/321441", "https://ndownloader.figshare.com/files/321472", "https://ndownloader.figshare.com/files/321497", "https://ndownloader.figshare.com/files/321516", "https://ndownloader.figshare.com/files/321536", "https://ndownloader.figshare.com/files/321558"], "description"=>"<div><p>With rapid advances in the development of DNA sequencing technologies, a plethora of high-throughput genome and proteome data from a diverse spectrum of organisms have been generated. The functional annotation and evolutionary history of proteins are usually inferred from domains predicted from the genome sequences. Traditional database-based domain prediction methods cannot identify novel domains, however, and alignment-based methods, which look for recurring segments in the proteome, are computationally demanding. Here, we propose a novel genome-wide domain prediction method, SECOM. Instead of conducting all-against-all sequence alignment, SECOM first indexes all the proteins in the genome by using a hash seed function. Local similarity can thus be detected and encoded into a graph structure, in which each node represents a protein sequence and each edge weight represents the shared hash seeds between the two nodes. SECOM then formulates the domain prediction problem as an overlapping community-finding problem in this graph. A backward graph percolation algorithm that efficiently identifies the domains is proposed. We tested SECOM on five recently sequenced genomes of aquatic animals. Our tests demonstrated that SECOM was able to identify most of the known domains identified by InterProScan. When compared with the alignment-based method, SECOM showed higher sensitivity in detecting putative novel domains, while it was also three orders of magnitude faster. For example, SECOM was able to predict a novel sponge-specific domain in nucleoside-triphosphatase (NTPases). Furthermore, SECOM discovered two novel domains, likely of bacterial origin, that are taxonomically restricted to sea anemone and hydra. SECOM is an open-source program and available at <a href=\"http://sfb.kaust.edu.sa/Pages/Software.aspx\">http://sfb.kaust.edu.sa/Pages/Software.aspx</a>.</p> </div>", "links"=>[], "tags"=>["hash", "detection", "based-approach", "genome-scale"], "article_id"=>123365, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Ming Fan", "Ka-Chun Wong", "Taewoo Ryu", "Timothy Ravasi", "Xin Gao"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039475.s001", "https://dx.doi.org/10.1371/journal.pone.0039475.s002", "https://dx.doi.org/10.1371/journal.pone.0039475.s003", "https://dx.doi.org/10.1371/journal.pone.0039475.s004", "https://dx.doi.org/10.1371/journal.pone.0039475.s005", "https://dx.doi.org/10.1371/journal.pone.0039475.s006", "https://dx.doi.org/10.1371/journal.pone.0039475.s007", "https://dx.doi.org/10.1371/journal.pone.0039475.s008", "https://dx.doi.org/10.1371/journal.pone.0039475.s009", "https://dx.doi.org/10.1371/journal.pone.0039475.s010", "https://dx.doi.org/10.1371/journal.pone.0039475.s011", "https://dx.doi.org/10.1371/journal.pone.0039475.s012", "https://dx.doi.org/10.1371/journal.pone.0039475.s013", "https://dx.doi.org/10.1371/journal.pone.0039475.s014", "https://dx.doi.org/10.1371/journal.pone.0039475.s015"], "stats"=>{"downloads"=>27, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/SECOM_A_Novel_Hash_Seed_and_Community_Detection_Based_Approach_for_Genome_Scale_Protein_Domain_Identification/123365", "title"=>"SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-06-28 00:56:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/617288"], "description"=>"<p>All the recall, precision and F1 score values are given as percentiles. DIV denotes DIVCLUS and SEC denotes SECOM.</p>", "links"=>[], "tags"=>["secom", "divclus", "sponge"], "article_id"=>287777, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Ming Fan", "Ka-Chun Wong", "Taewoo Ryu", "Timothy Ravasi", "Xin Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039475.t002", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Revised_performance_SECOM_and_DIVCLUS_on_the_sponge_proteome_/287777", "title"=>"Revised performance SECOM and DIVCLUS on the sponge proteome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-28 02:09:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/617255"], "description"=>"<p>All the recall, precision and F1 score values are percentiles. DIV denotes DIVCLUS and SEC denotes SECOM.</p>", "links"=>[], "tags"=>["secom", "divclus", "aquatic"], "article_id"=>287743, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Ming Fan", "Ka-Chun Wong", "Taewoo Ryu", "Timothy Ravasi", "Xin Gao"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039475.t001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overall_performance_of_SECOM_and_DIVCLUS_on_the_five_aquatic_proteomes_/287743", "title"=>"Overall performance of SECOM and DIVCLUS on the five aquatic proteomes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-28 02:09:03"}

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Relative Metric

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