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Seqcrawler: biological data indexing and browsing platform

Olivier Sallou, Anthony Bretaudeau, Aurelien Roult
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
It has been successfully tested in a private cloud with 3 index shards (pieces of index) hosting~400 millions of sequence information (whole GenBank, UniProt, PDB and others) for a total size of 600 GB  ...  Results: The software is scalable from a single computer to a cloud-based infrastructure.  ...  Components Indexer The indexer program is a set of Perl/Java command-line tools used to load a document (see supported formats), containing meta-data and/or data (DNA sequences for example), in the search  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-13-175">doi:10.1186/1471-2105-13-175</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22827839">pmid:22827839</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3481441/">pmcid:PMC3481441</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vno6gfnms5b6pkebnuroohzz6y">fatcat:vno6gfnms5b6pkebnuroohzz6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170819220918/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-175?site=bmcbioinformatics.biomedcentral.com" 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/70/9b70b45eecb09df2d4bb6ff7bc1b2efb816362d6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-13-175"> <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/PMC3481441" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Benchmarking a Many-Core Neuromorphic Platform With an MPI-Based DNA Sequence Matching Algorithm

Gianvito Urgese, Francesco Barchi, Emanuele Parisi, Evelina Forno, Andrea Acquaviva, Enrico Macii
<span title="2019-11-14">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ikdpfme5h5egvnwtvvtjrnntyy" style="color: black;">Electronics</a> </i> &nbsp;
In this paper, we present an implementation of a parallel DNA sequence matching algorithm implemented by using the MPI programming paradigm ported to the SpiNNaker platform.  ...  Exploiting this application, we benchmarked the SpiNNaker platform in terms of scalability and synchronisation latency.  ...  multiscale computation in neuromorphic hybrid systems FED Fast string matching method for Encoded DNA sequences  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/electronics8111342">doi:10.3390/electronics8111342</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yjsmlxwqtrh2pht53mcz3wux2e">fatcat:yjsmlxwqtrh2pht53mcz3wux2e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191116031016/https://res.mdpi.com/d_attachment/electronics/electronics-08-01342/article_deploy/electronics-08-01342.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/97/4c/974c25bfe29d630624f0deac101f9a811f0afe1b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/electronics8111342"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

SEQUENCE SIMILARITY SEARCH USING DISCRETE FOURIER AND WAVELET TRANSFORMATION TECHNIQUES

S. ALIREZA AGHILI, DIVYAKANT AGRAWAL, AMR EL ABBADI
<span title="">2005</span> <i title="World Scientific Pub Co Pte Lt"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bmgus4fa7vg37kpnbuixwilqf4" style="color: black;">International journal on artificial intelligence tools</a> </i> &nbsp;
In this paper, we study the problem of sequence similarity search.  ...  In this paper, we study the problem of sequence similarity search.  ...  Background, Related Work In a typical application of similarity search range query, given a protein or DNA query sequence Q and range r, it is compared with all the sequences in the database in search  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/s0218213005002363">doi:10.1142/s0218213005002363</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yaekmngeoreybllchog7vth24e">fatcat:yaekmngeoreybllchog7vth24e</a> </span>
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Workload characterization for MG-RAST metagenomic data analytics service in the cloud

Wei Tang, Jared Bischof, Narayan Desai, Kanak Mahadik, Wolfgang Gerlach, Travis Harrison, Andreas Wilke, Folker Meyer
<span title="">2014</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/faqqmambavbalpofpx3p6nntua" style="color: black;">2014 IEEE International Conference on Big Data (Big Data)</a> </i> &nbsp;
The cost of DNA sequencing has plummeted in recent years. The consequent data deluge has imposed big burdens for data analysis applications.  ...  In this paper, we characterize the MG-RAST workloads running in the cloud, from the perspectives of computation, I/O, and data transfer.  ...  ACKNOWLEDGMENTS This work was supported in part by the NIH award U01HG006537 "OSDF: Support infrastructure for NextGen sequence storage, analysis, and management", and U.S.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/bigdata.2014.7004394">doi:10.1109/bigdata.2014.7004394</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/bigdataconf/TangBDMGHWM14.html">dblp:conf/bigdataconf/TangBDMGHWM14</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4qcliocqhbfyxam2ch26dmst2u">fatcat:4qcliocqhbfyxam2ch26dmst2u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20151110082529/http://www.mcs.anl.gov/papers/P5202-0914.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/fc/1a/fc1a88225e6d975d5a03917de41abc66d7a87b8a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/bigdata.2014.7004394"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Using MoBIoS' scalable genome join to find conserved primer pair candidates between two genomes

W. Xu, W. J. Briggs, J. Padolina, R. E. Timme, W. Liu, C. R. Linder, D. P. Miranker
<span title="2004-07-19">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Motivation: For the purpose of identifying evolutionary reticulation events in flowering plants, we determine a large number of paired, conserved DNA oligomers that may be used as primers to amplify orthologous  ...  DNA regions using the polymerase chain reaction (PCR).  ...  This research was supported in part by grants from NSF: DBI-0241180, IIS-0325116, EIA-0121680 and EF-0331453.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth929">doi:10.1093/bioinformatics/bth929</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15262820">pmid:15262820</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gjmucr6cijb6jkcsu6nx5voo7u">fatcat:gjmucr6cijb6jkcsu6nx5voo7u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223052642/http://pdfs.semanticscholar.org/4277/907c10d7661704fe0ef358783bab7ded019c.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/42/77/4277907c10d7661704fe0ef358783bab7ded019c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth929"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Intelligent System for Ranking Big Data in Search Engine

and Ibrahim M. EL-Hasnony1 M.M.El-Gayar 1
<span title="2021-08-15">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
DNA consists of a large sequence of a specific set of string characters (e.g. ACGT) where this method measures the degree of similarity by aligning two entire sequences.  ...  in some standard search engines.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5202916">doi:10.5281/zenodo.5202916</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/azrj2u5jkrcktaoyd6tkjm73ly">fatcat:azrj2u5jkrcktaoyd6tkjm73ly</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210816160237/https://zenodo.org/record/5202917/files/Intelligent%20System%20for%20Ranking%20Big%20Data%20in%20Search%20Engine.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/d6/cc/d6cc0c35813307a928e6404952346145b2a75dee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5202916"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Creating the CIPRES Science Gateway for inference of large phylogenetic trees

Mark A. Miller, Wayne Pfeiffer, Terri Schwartz
<span title="">2010</span> <i title="IEEE"> 2010 Gateway Computing Environments Workshop (GCE) </i> &nbsp;
Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to  ...  Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation.  ...  ACKNOWLEDGEMENTS This work was supported in part by National Science Foundation awards NSF EF 01-31648 (MM and TS) and OCI-932251 (WP) as well as National Institutes of Health award 5R01GM073931 (MM).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/gce.2010.5676129">doi:10.1109/gce.2010.5676129</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/422v4kiydbhuflsvpclngtusmm">fatcat:422v4kiydbhuflsvpclngtusmm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20161215181826/http://www.phylo.org:80/sub_sections/portal/sc2010_paper.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/e2/7a/e27acaf97f5b2eae4257bb5d8278fbe0e6405c39.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/gce.2010.5676129"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Countering GATTACA

Pierre Baldi, Roberta Baronio, Emiliano De Cristofaro, Paolo Gasti, Gene Tsudik
<span title="">2011</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rau5643b7ncwvh74y6p64hntle" style="color: black;">Proceedings of the 18th ACM conference on Computer and communications security - CCS &#39;11</a> </i> &nbsp;
Recent advances in DNA sequencing technologies have put ubiquitous availability of fully sequenced human genomes within reach.  ...  It is no longer hard to imagine the day when everyone will have the means to obtain and store one's own DNA sequence.  ...  A number of cryptographic protocols have been proposed for private searching, matching and evaluating similarity of strings, including DNA sequences.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2046707.2046785">doi:10.1145/2046707.2046785</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/ccs/BaldiBCGT11.html">dblp:conf/ccs/BaldiBCGT11</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/le7xzcowz5dv7e32egaai5pkbq">fatcat:le7xzcowz5dv7e32egaai5pkbq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190217071029/https://static.aminer.org/pdf/20170130/pdfs/ccs/npn6gezkyko8jt9xw3sdezjfwvqtu0dm.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/e4/41/e441a2318068ac59064fe91f7ba375d418a6a317.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2046707.2046785"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Refining the r-index [article]

Hideo Bannai, Travis Gagie, Tomohiro I
<span title="2019-07-04">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In this paper we first strengthen and simplify Policriti and Prezza's Toehold Lemma (DCC '16; Algorithmica, 2017), which inspired the r-index and plays an important role in its implementation.  ...  Gagie, Navarro and Prezza's r-index (SODA, 2018) promises to speed up DNA alignment and variation calling by allowing us to index entire genomic databases, provided certain obstacles can be overcome.  ...  We tested on the datasets used in [13] (and available in [23] ). • DNA: A pseudo-real DNA sequence consisting of 629145 copies of a DNA sequence of length 1000 where each character was mutated with  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1802.05906v6">arXiv:1802.05906v6</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kwrlyfjyfrfhjocdzlemph6kiy">fatcat:kwrlyfjyfrfhjocdzlemph6kiy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200904113746/https://arxiv.org/pdf/1802.05906v5.pdf" title="fulltext PDF download [not primary version]" 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] <span style="color: #f43e3e;">&#10033;</span> <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/33/f1/33f1c72912c1e22165bbd8b3f2c46fd739b15eaa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1802.05906v6" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database

Daniel J Park, Tú Nguyen-Dumont, Sori Kang, Karin Verspoor, Bernard J Pope
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/phbrgpflarcnrjkwyvkg46nvtu" style="color: black;">Source Code for Biology and Medicine</a> </i> &nbsp;
The NCBI Entrez online web-search interface is convenient for simple manual search for a small number of genes but impractical for the kinds of outputs seen in typical genomics projects.  ...  We applied Annokey to the entire human Entrez Gene database using the key-term "DNA repair" and assessed its performance in identifying the 176 members of a published "gold standard" list of genes established  ...  Background Recent advances in high-throughput DNA sequencing have allowed large regions of a sample genome (or genomes) to be sequenced rapidly at high coverage [1] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1751-0473-9-15">doi:10.1186/1751-0473-9-15</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4106183/">pmcid:PMC4106183</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uecbrdd7tzbadgtzc5myg7ibci">fatcat:uecbrdd7tzbadgtzc5myg7ibci</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809160432/https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-9-15?site=scfbm.biomedcentral.com" 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/0a/9b0a194e35919f027bfcb39aad7b8c785b03396e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1751-0473-9-15"> <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/PMC4106183" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Study on Efficient Way to Identify User Aware Rare Sequential Pattern Matching in Document Stream

Swati V. Mengje
<span title="2017-02-28">2017</span> <i title="International Journal for Research in Applied Science and Engineering Technology (IJRASET)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hsp44774azcezeyiq4kuzpfh5a" style="color: black;">International Journal for Research in Applied Science and Engineering Technology</a> </i> &nbsp;
Sequential Topic Patterns (URSTPs) in document streams on the Internet.  ...  In this paper, in order to characterize and detect personalized and abnormal behaviours of Internet users, we propose Sequential Topic Patterns (STPs) and formulate the problem of mining User-aware Rare  ...  faults which in turn allows various insertions, deletions, and mutations in DNA sequences, and handling industry or engineering sequential process analysis are interesting issues for future research.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.22214/ijraset.2017.2019">doi:10.22214/ijraset.2017.2019</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s543g4e5gbaavcylwlqh73glyy">fatcat:s543g4e5gbaavcylwlqh73glyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180602161244/http://www.ijraset.com/fileserve.php?FID=6209" 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/a0/4f/a04fbd621eec99a5c9511929b25f683fce2cab97.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.22214/ijraset.2017.2019"> <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>

ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher level analysis of closely related bacterial isolates

Oliver Schwengers, Andreas Hoek, Moritz Fritzenwanker, Linda Falgenhauer, Torsten Hain, Trinad Chakraborty, Alexander Goesmann, Mihaela Pertea
<span title="2020-03-05">2020</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Advances in DNA sequencing technologies and continuously dropping costs have resulted in a tremendous increase in the amounts of available sequence data.  ...  Whole genome sequencing of bacteria has become daily routine in many fields.  ...  Furthermore, we believe that the utilization of portable devices for DNA sequencing will shift analysis from central software installations to either decentral offline tools or scalable cloud solutions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1007134">doi:10.1371/journal.pcbi.1007134</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32134915">pmid:32134915</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j6vcr3ieavh2xggwzbju7naoqe">fatcat:j6vcr3ieavh2xggwzbju7naoqe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200307080349/https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007134&amp;type=printable" 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/75/c1/75c1141b388d8b0c223fabdc82357b8e43fb88d8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1007134"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

Countering Gattaca: Efficient and Secure Testing of Fully-Sequenced Human Genomes (Full Version) [article]

Pierre Baldi, Roberta Baronio, Emiliano De Cristofaro, Paolo Gasti, Gene Tsudik
<span title="2011-12-01">2011</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Recent advances in DNA sequencing technologies have put ubiquitous availability of fully sequenced human genomes within reach.  ...  It is no longer hard to imagine the day when everyone will have the means to obtain and store one's own DNA sequence.  ...  Work of Pierre Baldi is supported, in part, by grants: NIH LM010235 and NIH-NLM T15 LM07443.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1110.2478v3">arXiv:1110.2478v3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ymnvydahu5fpnfh37lp35rbja4">fatcat:ymnvydahu5fpnfh37lp35rbja4</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/arxiv-1110.2478/1110.2478.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> File Archive [PDF] </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1110.2478v3" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

A dynamic run-profile energy-aware approach for scheduling computationally intensive bioinformatics applications

Sachin Pawaskar, Hesham H. Ali
<span title="">2016</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfatt7tua5aatozu2id5rdeuti" style="color: black;">2016 International Conference on High Performance Computing &amp; Simulation (HPCS)</a> </i> &nbsp;
In the Offline Phase, we use a run profile based approach to generate the initial schedule.  ...  in the Offline phase has an impact on the energy optimization achieved by the EAS algorithm.  ...  Work using BLAST search can be characterized by the data approach used in the search which is of the following 2 main types. 1) Query segmentation method -partitions the sequence query set.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/hpcsim.2016.7568366">doi:10.1109/hpcsim.2016.7568366</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/ieeehpcs/PawaskarA16.html">dblp:conf/ieeehpcs/PawaskarA16</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qcwrmyayy5eihay5qiw2prkam4">fatcat:qcwrmyayy5eihay5qiw2prkam4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200319220642/https://digitalcommons.unomaha.edu/cgi/viewcontent.cgi?referer=&amp;httpsredir=1&amp;article=1046&amp;context=compsicfacproc" 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/51/5a/515ad59f3e304f89584e759a08b8cf8826f58b80.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/hpcsim.2016.7568366"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

BioCyBig: A Cyberphysical System for Integrative Microfluidics-Driven Analysis of Genomic Association Studies

Mohamed Ibrahim, Krishnendu Chakrabarty, Jun Zeng
<span title="">2016</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zfau6furxjhwdi5ecdqcdfbrbq" style="color: black;">IEEE Transactions on Big Data</a> </i> &nbsp;
A case study from cancer research is discussed to explain the significance of our framework in promoting coordinated genomic studies.  ...  This framework therefore leads to a better understanding of diseases such as cancer, and helps researchers in identifying effective treatments.  ...  Notably, the DNA sequences involved in the establishment of proteins are said to be "expressed genes".  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tbdata.2016.2643683">doi:10.1109/tbdata.2016.2643683</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u5ws25dwdnbmbj4bb4qyppbl2a">fatcat:u5ws25dwdnbmbj4bb4qyppbl2a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303191437/http://people.duke.edu:80/~msi3/Papers/TBD_2016.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/c6/93/c6934b99ce3b2f6b4d3ab02cf8ef145095533ac6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tbdata.2016.2643683"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>
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