Pub Date : 2022-05-19DOI: 10.1186/s13015-022-00218-8
Marcin Wawerka, D. Dabkowski, Natalia Rutecka, Agnieszka Mykowiecka, P. Górecki
{"title":"Embedding gene trees into phylogenetic networks by conflict resolution algorithms","authors":"Marcin Wawerka, D. Dabkowski, Natalia Rutecka, Agnieszka Mykowiecka, P. Górecki","doi":"10.1186/s13015-022-00218-8","DOIUrl":"https://doi.org/10.1186/s13015-022-00218-8","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"76 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78686342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-05-16DOI: 10.1186/s13015-022-00219-7
Peter F. Stadler, S. Will
{"title":"Bi-alignments with affine gaps costs","authors":"Peter F. Stadler, S. Will","doi":"10.1186/s13015-022-00219-7","DOIUrl":"https://doi.org/10.1186/s13015-022-00219-7","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"1 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2022-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82802988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-03-29DOI: 10.1186/s13015-022-00215-x
Patrick Kunzmann, Jacob Marcel Anter, K. Hamacher
{"title":"Adding hydrogen atoms to molecular models via fragment superimposition","authors":"Patrick Kunzmann, Jacob Marcel Anter, K. Hamacher","doi":"10.1186/s13015-022-00215-x","DOIUrl":"https://doi.org/10.1186/s13015-022-00215-x","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2022-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65741668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-03-14DOI: 10.1186/s13015-022-00209-9
P. Sashittal, Simone Zaccaria, M. El-Kebir
{"title":"Parsimonious Clone Tree Integration in cancer","authors":"P. Sashittal, Simone Zaccaria, M. El-Kebir","doi":"10.1186/s13015-022-00209-9","DOIUrl":"https://doi.org/10.1186/s13015-022-00209-9","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2022-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86681252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-05-04DOI: 10.1186/s13015-022-00213-z
Bertrand Marchand, Y. Ponty, L. Bulteau
{"title":"Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics","authors":"Bertrand Marchand, Y. Ponty, L. Bulteau","doi":"10.1186/s13015-022-00213-z","DOIUrl":"https://doi.org/10.1186/s13015-022-00213-z","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2021-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65742120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-11-15eCollection Date: 2019-01-01DOI: 10.1186/s13015-019-0157-4
Christophe Ambroise, Alia Dehman, Pierre Neuvial, Guillem Rigaill, Nathalie Vialaneix
Background: Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-resolution, locus-level measurements. An intuitive way of doing this is to perform a modified Hierarchical Agglomerative Clustering (HAC), where only adjacent clusters (according to the ordering of positions within a chromosome) are allowed to be merged. But a major practical drawback of this method is its quadratic time and space complexity in the number of loci, which is typically of the order of to for each chromosome.
Results: By assuming that the similarity between physically distant objects is negligible, we are able to propose an implementation of adjacency-constrained HAC with quasi-linear complexity. This is achieved by pre-calculating specific sums of similarities, and storing candidate fusions in a min-heap. Our illustrations on GWAS and Hi-C datasets demonstrate the relevance of this assumption, and show that this method highlights biologically meaningful signals. Thanks to its small time and memory footprint, the method can be run on a standard laptop in minutes or even seconds.
Availability and implementation: Software and sample data are available as an R package, adjclust, that can be downloaded from the Comprehensive R Archive Network (CRAN).
{"title":"Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics.","authors":"Christophe Ambroise, Alia Dehman, Pierre Neuvial, Guillem Rigaill, Nathalie Vialaneix","doi":"10.1186/s13015-019-0157-4","DOIUrl":"https://doi.org/10.1186/s13015-019-0157-4","url":null,"abstract":"<p><strong>Background: </strong>Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-resolution, locus-level measurements. An intuitive way of doing this is to perform a modified Hierarchical Agglomerative Clustering (HAC), where only adjacent clusters (according to the ordering of positions within a chromosome) are allowed to be merged. But a major practical drawback of this method is its quadratic time and space complexity in the number of loci, which is typically of the order of <math><msup><mn>10</mn> <mn>4</mn></msup> </math> to <math><msup><mn>10</mn> <mn>5</mn></msup> </math> for each chromosome.</p><p><strong>Results: </strong>By assuming that the similarity between physically distant objects is negligible, we are able to propose an implementation of adjacency-constrained HAC with quasi-linear complexity. This is achieved by pre-calculating specific sums of similarities, and storing candidate fusions in a min-heap. Our illustrations on GWAS and Hi-C datasets demonstrate the relevance of this assumption, and show that this method highlights biologically meaningful signals. Thanks to its small time and memory footprint, the method can be run on a standard laptop in minutes or even seconds.</p><p><strong>Availability and implementation: </strong>Software and sample data are available as an R package, <b>adjclust</b>, that can be downloaded from the Comprehensive R Archive Network (CRAN).</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"14 ","pages":"22"},"PeriodicalIF":1.0,"publicationDate":"2019-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-019-0157-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49684571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-09-15DOI: 10.1186/s13015-016-0086-4
J. Ambroise, Jamal Badir, Louise Nienhaus, Annie Robert, A. Dekairelle, J. Gala
{"title":"Using a constraint-based regression method for relative quantification of somatic mutations in pyrosequencing signals: a case for NRAS analysis","authors":"J. Ambroise, Jamal Badir, Louise Nienhaus, Annie Robert, A. Dekairelle, J. Gala","doi":"10.1186/s13015-016-0086-4","DOIUrl":"https://doi.org/10.1186/s13015-016-0086-4","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"11 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2016-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-016-0086-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65742106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-02-24DOI: 10.1186/s13015-016-0063-y
H. Indrischek, Nicolas Wieseke, Peter F. Stadler, Sonja J. Prohaska
{"title":"The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies","authors":"H. Indrischek, Nicolas Wieseke, Peter F. Stadler, Sonja J. Prohaska","doi":"10.1186/s13015-016-0063-y","DOIUrl":"https://doi.org/10.1186/s13015-016-0063-y","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"78 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2016-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-016-0063-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65742096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-12-01DOI: 10.1186/s13015-015-0062-4
Jongpill Choi, Kiejung Park, S. Cho, Myungguen Chung
{"title":"HIA: a genome mapper using hybrid index-based sequence alignment","authors":"Jongpill Choi, Kiejung Park, S. Cho, Myungguen Chung","doi":"10.1186/s13015-015-0062-4","DOIUrl":"https://doi.org/10.1186/s13015-015-0062-4","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"10 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-015-0062-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65742084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-12-01DOI: 10.1186/s13015-015-0061-5
Katja Reichel, Valentin Bahier, C. Midoux, N. Parisey, J. Masson, S. Stoeckel
{"title":"Interpretation and approximation tools for big, dense Markov chain transition matrices in population genetics","authors":"Katja Reichel, Valentin Bahier, C. Midoux, N. Parisey, J. Masson, S. Stoeckel","doi":"10.1186/s13015-015-0061-5","DOIUrl":"https://doi.org/10.1186/s13015-015-0061-5","url":null,"abstract":"","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"10 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13015-015-0061-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65742048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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