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An Improved Search Algorithm for Optimal Multiple-Sequence Alignment

S. Schroedl
<span title="2005-05-01">2005</span> <i title="AI Access Foundation"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4ax4efcwajcgvidb6hcg6mwx4a" style="color: black;">The Journal of Artificial Intelligence Research</a> </i> &nbsp;
Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to push the limits of exact algorithms further.  ...  Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology.  ...  Acknowledgments The author would like to thank the reviewers of this article whose comments have helped in significantly improving it.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1613/jair.1534">doi:10.1613/jair.1534</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7uhk7wabxrgnpdrbwspujnji3u">fatcat:7uhk7wabxrgnpdrbwspujnji3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228095352/http://pdfs.semanticscholar.org/a092/982b056404dc5cea0e73b4aae083ab38e2a6.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a0/92/a092982b056404dc5cea0e73b4aae083ab38e2a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1613/jair.1534"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

CUDAlign 4.0: Incremental Speculative Traceback for Exact Chromosome-Wide Alignment in GPU Clusters

Edans Flavius de Oliveira Sandes, Guillermo Miranda, Xavier Martorell, Eduard Ayguade, George Teodoro, Alba Cristina Magalhaes Melo
<span title="2016-10-01">2016</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ll6bfs5o6bahfinh3u5z2cnyoy" style="color: black;">IEEE Transactions on Parallel and Distributed Systems</a> </i> &nbsp;
This paper proposes and evaluates CUDAlign 4.0, a parallel strategy to obtain the optimal alignment of huge DNA sequences in multi-GPU platforms, using the exact Smith-Waterman (SW) algorithm.  ...  As far as we know, this is the first time such comparison was made with the SW exact method.  ...  ACKNOWLEDGEMENTS We thankfully acknowledge the support of the grant SEV-2015-0493 of Severo Ochoa Program, awarded by the Spanish Government, PHBP14/00081(Programa Hispano-Brasileno) of the Spanish Ministry  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tpds.2016.2515597">doi:10.1109/tpds.2016.2515597</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pk3nptrmoberdl3rocjmv5yoiy">fatcat:pk3nptrmoberdl3rocjmv5yoiy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719101933/https://upcommons.upc.edu/bitstream/handle/2117/99741/CUDAlign+4.0+Incremental+Speculative.pdf;jsessionid=BDB2468A52D38D9A3CFC3B1D5F120D31?sequence=6" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7f/0e/7f0e4030d3b47b9616455c088bb375a8b2338dde.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tpds.2016.2515597"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Mining Low-Variance Biclusters to Discover Coregulation Modules in Sequencing Datasets

Zhen Hu, Raj Bhatnagar
<span title="">2012</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fw4azkpu65d2thmrwfkoawyxse" style="color: black;">Scientific Programming</a> </i> &nbsp;
The ideal biclusters generated would contain subsets of genes and transcription factors (TF) such that the cell-values in biclusters are distributed around a mean value with very low variance.  ...  In this paper we present an algorithm that searches a space of all overlapping biclusters organized in a lattice, and uses an upper bound on variance values of biclusters as the guiding metric.  ...  Pruning To reduce the computational cost of the search, we employ a number of pruning strategies while guaranteeing that all interesting biclusters will still be retained.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2012/953863">doi:10.1155/2012/953863</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rair5mqdibef3eimhckhetu7tm">fatcat:rair5mqdibef3eimhckhetu7tm</a> </span>
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Algorithm for low-variance biclusters to identify coregulation modules in sequencing datasets

Zhen Hu, Raj Bhatnagar
<span title="">2011</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fqqihtxlu5bvfaqxjyvqcob35a" style="color: black;">Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics - BIOKDD &#39;11</a> </i> &nbsp;
The ideal biclusters generated should contain subsets of genes, and transcription factors (TF) such that the cell-values in biclusters are distributed around a mean value with low variance.  ...  High-throughput sequencing (CHIP-Seq) data exhibit binding events with possible binding locations and their strengths, followed by interpretations of the locations of peaks.  ...  For example, in figure 2 (b) < {g1, Pruning To reduce the computational cost of the search, we employ a number of pruning strategies while still guaranteeing that all interesting biclusters will  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2003351.2003352">doi:10.1145/2003351.2003352</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/kdd/HuB11.html">dblp:conf/kdd/HuB11</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wxkp4sxzl5hr7pfdi5gclyg5cq">fatcat:wxkp4sxzl5hr7pfdi5gclyg5cq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811214138/http://www.cs.rpi.edu/~zaki/Workshops/BIOKDD11/doc/biokdd2011_Zhen.Hu.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/07/fe/07fe856cdd39fff8a5155f5960aaac41d6d938a5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2003351.2003352"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Permu-pattern

Meng Hu, Jiong Yang, Wei Su
<span title="">2008</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fqqihtxlu5bvfaqxjyvqcob35a" style="color: black;">Proceeding of the 14th ACM SIGKDD international conference on Knowledge discovery and data mining - KDD 08</a> </i> &nbsp;
Pattern discovery in sequences is an important problem in many applications, especially in computational biology and text mining.  ...  A large amount of synthetic data is also utilized to demonstrate the efficiency of the Permu-pattern algorithm.  ...  In the worst case, the pruning may not reduce the number of candidate patterns significantly.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1401890.1401932">doi:10.1145/1401890.1401932</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/kdd/HuYS08.html">dblp:conf/kdd/HuYS08</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ioseqn7qrvflllo232s4h32s7a">fatcat:ioseqn7qrvflllo232s4h32s7a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100613044418/http://vorlon.case.edu/~jiong/research/papers/rtp92-hu.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/32/b1/32b1ec7726fbf65c84e84dda084cf43a15451dac.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1401890.1401932"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Ultra-fast genome comparison for large-scale genomic experiments

Esteban Pérez-Wohlfeil, Sergio Diaz-del-Pino, Oswaldo Trelles
<span title="2019-07-16">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
The method produces both a previsualization of the comparison and a collection of indices to drastically reduce computational complexity when performing exhaustive comparisons.  ...  Last, the method scores the comparison to automate classification of sequences and produces a list of detected synteny blocks to enable new evolutionary studies.  ...  and ISCIII-PT17.0009.0022), the Instituto de Investigación Biomédica de Málaga IBIMA and the University of Málaga.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-019-46773-w">doi:10.1038/s41598-019-46773-w</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31312019">pmid:31312019</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6635410/">pmcid:PMC6635410</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zqlawtkpzzewtinupv2zwrkie4">fatcat:zqlawtkpzzewtinupv2zwrkie4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191102141009/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6635410&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/30/a3/30a3b55ec95621b0145df990f79af92a86cd1ac7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-019-46773-w"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6635410" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Distance-join

Lei Zou, Lei Chen, M. Tamer Özsu
<span title="2009-08-01">2009</span> <i title="VLDB Endowment"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p6rqwwpkkjbcldejepcehaalby" style="color: black;">Proceedings of the VLDB Endowment</a> </i> &nbsp;
In order to reduce the search space significantly, we first transform the vertices into points in a vector space via graph embedding techniques, coverting a pattern match query into a distance-based multi-way  ...  ., query Q), we want to find all matches (in G) that have the similar connections as those in Q.  ...  In this section, we discuss the cost of D-join algorithm that answers edge query, which has three components: the cost of block nested loop join (Lines 2-10 in Algorithm 2), the cost of computing the exact  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14778/1687627.1687727">doi:10.14778/1687627.1687727</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mloztyf765ftrdlm6ilbpwuxcu">fatcat:mloztyf765ftrdlm6ilbpwuxcu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110516200744/http://www.vldb.org/pvldb/2/vldb09-876.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9b/8b/9b8bee775562b96b8202cda43ad9cd4dd82c1ef4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14778/1687627.1687727"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

SING: Subgraph search In Non-homogeneous Graphs

Raffaele Di Natale, Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dennis Shasha
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Conclusions: Extensive tests on chemical compounds, biological networks and synthetic graphs show that the proposed system outperforms the most popular systems in query time over databases of medium and  ...  The method uses the notion of feature, which can be a small subgraph, subtree or path. Each graph in the database is annotated with the set of all its features.  ...  Acknowledgements We would like to thank the authors of gIndex, CTree and GCoding for having kindly provided their tools for comparison purpose.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-96">doi:10.1186/1471-2105-11-96</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20170516">pmid:20170516</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2850364/">pmcid:PMC2850364</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lqr4jrkwb5gjzeu4fnsvfbkouu">fatcat:lqr4jrkwb5gjzeu4fnsvfbkouu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170819153440/https://www.biomedcentral.com/content/pdf/1471-2105-11-96.pdf&amp;keyword=Biased-Information-Search-in-Homogeneous-Groups-" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0c/88/0c88fb876b51ca36e74240db70465b426335a8f3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-96"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850364" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Short Read Mapping: An Algorithmic Tour

Stefan Canzar, Steven L. Salzberg
<span title="">2017</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yfvtieuumfamvmjlc255uckdlm" style="color: black;">Proceedings of the IEEE</a> </i> &nbsp;
Index Terms sequence alignment; string matching; suffix trees; Burrows-Wheeler transform; DNA sequencing The first elegant algorithm to compute the optimal alignment of two sequences, in some sense the  ...  In this perspective, we describe these efforts and the current state of the art in NGS alignment algorithms.  ...  Acknowledgments This work was supported in part by the U.S. National Institutes of Health under grant R01 HG006102 to SLS. Stefan Canzar received his Diploma in Computer  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/jproc.2015.2455551">doi:10.1109/jproc.2015.2455551</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28502990">pmid:28502990</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5425171/">pmcid:PMC5425171</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ic6d6z5ggbazdkaotcotdtbo3u">fatcat:ic6d6z5ggbazdkaotcotdtbo3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200503234007/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5425171&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/97/3f/973f07bd295ae212830610753dd791053f9ff9c9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/jproc.2015.2455551"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425171" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Frequent pattern mining: current status and future directions

Jiawei Han, Hong Cheng, Dong Xin, Xifeng Yan
<span title="2007-01-27">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ja54f4dcmzfz7cvlo7o757jdba" style="color: black;">Data mining and knowledge discovery</a> </i> &nbsp;
In this article, we provide a brief overview of the current status of frequent pattern mining and discuss a few promising research directions.  ...  We believe that frequent pattern mining research has substantially broadened the scope of data analysis and will have deep impact on data mining methodologies and applications in the long run.  ...  The comparison also found that when there is a large number of frequent subsequences, all three algorithms run slowly.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10618-006-0059-1">doi:10.1007/s10618-006-0059-1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fpblaafhurfbtiimurret4idde">fatcat:fpblaafhurfbtiimurret4idde</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809033012/http://www.it.uu.se/edu/course/homepage/infoutv2/vt13/assignment_data/Han-fim-review.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7a/e0/7ae0cd2cf4468f813b5eccff9557c30294faaa58.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10618-006-0059-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Fixed-Parameter Algorithms in Phylogenetics

J. Gramm, A. Nickelsen, T. Tantau
<span title="2007-03-06">2007</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bf4qaipmsrghrjyxonrsmqevie" style="color: black;">Computer journal</a> </i> &nbsp;
We survey the use of fixed-parameter algorithms in the field of phylogenetics, which is the study of evolutionary relationships.  ...  The computation of phylogenies has applications in seemingly unrelated areas such as genomic sequencing and finding and understanding genes.  ...  This sequence is encoded in the genome using a sequence of codons (blocks of three bases) where each codon encodes one amino acid.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/comjnl/bxm049">doi:10.1093/comjnl/bxm049</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/txfzhsnt3zebffedefjbfacwue">fatcat:txfzhsnt3zebffedefjbfacwue</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808061539/http://www.tcs.uni-luebeck.de/downloads/papers/2008/survey.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/eb/7d/eb7dda43d769b7babe78218fcc96b4f9d385b16f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/comjnl/bxm049"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Fixed-Parameter Algorithms in Phylogenetics [chapter]

Jens Gramm, Arfst Nickelsen, Till Tantau
<span title="">2008</span> <i title="Humana Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
We survey the use of fixed-parameter algorithms in the field of phylogenetics, which is the study of evolutionary relationships.  ...  The computation of phylogenies has applications in seemingly unrelated areas such as genomic sequencing and finding and understanding genes.  ...  This sequence is encoded in the genome using a sequence of codons (blocks of three bases) where each codon encodes one amino acid.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-60327-159-2_24">doi:10.1007/978-1-60327-159-2_24</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18566780">pmid:18566780</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b7iiquxu5bcmxf776g4crrnepi">fatcat:b7iiquxu5bcmxf776g4crrnepi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808061539/http://www.tcs.uni-luebeck.de/downloads/papers/2008/survey.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/eb/7d/eb7dda43d769b7babe78218fcc96b4f9d385b16f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-60327-159-2_24"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Motif Discovery in Protein Sequences [chapter]

Salma Aouled El Haj Mohamed, Mourad Elloumi, Julie D. Thompson
<span title="2016-12-14">2016</span> <i title="InTech"> Pattern Recognition - Analysis and Applications </i> &nbsp;
The exponential increase in the size of the datasets produced by "next-generation sequencing" (NGS) poses unique computational challenges.  ...  They can occur in an exact or approximate form within a family or a subfamily of sequences.  ...  Acknowledgements We would like to thank the members of the BICS and BISTRO Bioinformatics Platforms in Strasbourg for their support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/65441">doi:10.5772/65441</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fefdhuhwrrfdhj2jtrjxvpzgq4">fatcat:fefdhuhwrrfdhj2jtrjxvpzgq4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501120348/https://cdn.intechopen.com/pdfs/52534.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/16/81/1681b90a64e3106838acbd6ae8a9d14ef21a694d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/65441"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

RASCAL: Calculation of Graph Similarity using Maximum Common Edge Subgraphs

J. W. Raymond
<span title="2002-06-01">2002</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bf4qaipmsrghrjyxonrsmqevie" style="color: black;">Computer journal</a> </i> &nbsp;
threshold, followed by a rigorous maximum common edge subgraph (MCES) detection algorithm to compute the exact degree and composition of similarity.  ...  The proposed MCES algorithm is based on a maximum clique formulation of the problem and is a significant improvement over other published algorithms.  ...  ACKNOWLEDGEMENTS The authors would like to extend their gratitude to Pfizer (Ann Arbor) for funding of this project  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/comjnl/45.6.631">doi:10.1093/comjnl/45.6.631</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/udp45d3ypvevdgxuvwgxpszh6e">fatcat:udp45d3ypvevdgxuvwgxpszh6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829132648/http://eprints.whiterose.ac.uk/3568/1/willets3.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bc/65/bc654bf968120d425a69b7ab220a01403d3b004a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/comjnl/45.6.631"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

A novel method to compare protein structures using local descriptors

Paweł Daniluk, Bogdan Lesyng
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Protein structure comparison is one of the most widely performed tasks in bioinformatics.  ...  Results: We present a novel method for protein structure comparison based on the formalism of local descriptors of protein structure -DEscriptor Defined Alignment (DEDAL).  ...  Acknowledgements Authors would like to thank Krzysztof Fidelis at the Genome Center, University of California, Davis for sharing ideas and help in improving the manuscript, and Andriy  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-344">doi:10.1186/1471-2105-12-344</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21849047">pmid:21849047</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3179968/">pmcid:PMC3179968</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/erpry2cujjakdpvfx4ke2hz2ta">fatcat:erpry2cujjakdpvfx4ke2hz2ta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20151104144501/http://www.biomedcentral.com/content/pdf/1471-2105-12-344.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e9/8a/e98a958fdb604f5e47d285b131af4ebf888f4e3f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-344"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179968" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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