Primer3_masker: integrating masking of template sequence with primer design software

Primer3_masker: integrating masking of template sequence with primer design software

Abstract Summary Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the genomes contain a large number of repeat sequences and other regions unsuitable for amplification by PCR. We have developed a novel k-mer based masking method that uses a statistical...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Bioinformatics 2018-06, Vol.34 (11), p.1937-1938
Hauptverfasser: Kõressaar, Triinu, Lepamets, Maarja, Kaplinski, Lauris, Raime, Kairi, Andreson, Reidar, Remm, Maido
Format: Artikel
Sprache:eng
Online-Zugang:Volltext bestellen
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 1938
container_issue 11
container_start_page 1937
container_title Bioinformatics
container_volume 34
creator Kõressaar, Triinu
Lepamets, Maarja
Kaplinski, Lauris
Raime, Kairi
Andreson, Reidar
Remm, Maido
description Abstract Summary Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the genomes contain a large number of repeat sequences and other regions unsuitable for amplification by PCR. We have developed a novel k-mer based masking method that uses a statistical model to detect and mask failure-prone regions on the DNA template prior to primer design. We implemented the software as a standalone software primer3_masker and integrated it into the primer design program Primer3. Availability and implementation The standalone version of primer3_masker is implemented in C. The source code is freely available at https://github.com/bioinfo-ut/primer3_masker/ (standalone version for Linux and macOS) and at https://github.com/primer3-org/primer3/ (integrated version). Primer3 web application that allows masking sequences of 196 animal and plant genomes is available at http://primer3.ut.ee/. Supplementary information Supplementary data are available at Bioinformatics online.
doi_str_mv 10.1093/bioinformatics/bty036
format Article
fullrecord <record><control><sourceid>proquest_TOX</sourceid><recordid>TN_cdi_proquest_miscellaneous_1990851999</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/bioinformatics/bty036</oup_id><sourcerecordid>1990851999</sourcerecordid><originalsourceid>FETCH-LOGICAL-c397t-dda528ee8446532e53bf0a4614690557677bc22227d01a3daf0ff76759e8c24e3</originalsourceid><addsrcrecordid>eNqNUE1PwzAMjRCIjcFPAOXIpZA2SdtwQxNf0iQ4jHOUts4I9Isk1bR_T0oHEjd8sC3rvWf7IXQek6uYCHpdmM60urON8qZ014XfEZoeoHnMUhIlhIvD0NM0i1hO6AydOPdOCI8ZY8dolgiaEsHTOVq_WNOApbJR7gPsDTath40Nou0Gj7Oxdhp7aPpaecAOPgdoS8Bb499w_83GFTizabHrtN8qC6foSKvawdm-LtDr_d16-Ritnh-elrerqKQi81FVKZ7kADljKacJcFpoolgaXhCE8yzNsqJMQmQViRWtlCZahykXkJcJA7pAl5Nub7twlfOyMa6EulYtdIOTsRAk5yGLAOUTtLSdcxa0HE9XdidjIkdD5V9D5WRo4F3sVwxFA9Uv68fBACAToBv6f2p-AStpiXg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1990851999</pqid></control><display><type>article</type><title>Primer3_masker: integrating masking of template sequence with primer design software</title><source>Oxford Journals Open Access Collection</source><creator>Kõressaar, Triinu ; Lepamets, Maarja ; Kaplinski, Lauris ; Raime, Kairi ; Andreson, Reidar ; Remm, Maido</creator><creatorcontrib>Kõressaar, Triinu ; Lepamets, Maarja ; Kaplinski, Lauris ; Raime, Kairi ; Andreson, Reidar ; Remm, Maido</creatorcontrib><description>Abstract Summary Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the genomes contain a large number of repeat sequences and other regions unsuitable for amplification by PCR. We have developed a novel k-mer based masking method that uses a statistical model to detect and mask failure-prone regions on the DNA template prior to primer design. We implemented the software as a standalone software primer3_masker and integrated it into the primer design program Primer3. Availability and implementation The standalone version of primer3_masker is implemented in C. The source code is freely available at https://github.com/bioinfo-ut/primer3_masker/ (standalone version for Linux and macOS) and at https://github.com/primer3-org/primer3/ (integrated version). Primer3 web application that allows masking sequences of 196 animal and plant genomes is available at http://primer3.ut.ee/. Supplementary information Supplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/bty036</identifier><identifier>PMID: 29360956</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><ispartof>Bioinformatics, 2018-06, Vol.34 (11), p.1937-1938</ispartof><rights>The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com 2018</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c397t-dda528ee8446532e53bf0a4614690557677bc22227d01a3daf0ff76759e8c24e3</citedby><cites>FETCH-LOGICAL-c397t-dda528ee8446532e53bf0a4614690557677bc22227d01a3daf0ff76759e8c24e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,1598,27901,27902</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bioinformatics/bty036$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29360956$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kõressaar, Triinu</creatorcontrib><creatorcontrib>Lepamets, Maarja</creatorcontrib><creatorcontrib>Kaplinski, Lauris</creatorcontrib><creatorcontrib>Raime, Kairi</creatorcontrib><creatorcontrib>Andreson, Reidar</creatorcontrib><creatorcontrib>Remm, Maido</creatorcontrib><title>Primer3_masker: integrating masking of template sequence with primer design software</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Abstract Summary Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the genomes contain a large number of repeat sequences and other regions unsuitable for amplification by PCR. We have developed a novel k-mer based masking method that uses a statistical model to detect and mask failure-prone regions on the DNA template prior to primer design. We implemented the software as a standalone software primer3_masker and integrated it into the primer design program Primer3. Availability and implementation The standalone version of primer3_masker is implemented in C. The source code is freely available at https://github.com/bioinfo-ut/primer3_masker/ (standalone version for Linux and macOS) and at https://github.com/primer3-org/primer3/ (integrated version). Primer3 web application that allows masking sequences of 196 animal and plant genomes is available at http://primer3.ut.ee/. Supplementary information Supplementary data are available at Bioinformatics online.</description><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><recordid>eNqNUE1PwzAMjRCIjcFPAOXIpZA2SdtwQxNf0iQ4jHOUts4I9Isk1bR_T0oHEjd8sC3rvWf7IXQek6uYCHpdmM60urON8qZ014XfEZoeoHnMUhIlhIvD0NM0i1hO6AydOPdOCI8ZY8dolgiaEsHTOVq_WNOApbJR7gPsDTath40Nou0Gj7Oxdhp7aPpaecAOPgdoS8Bb499w_83GFTizabHrtN8qC6foSKvawdm-LtDr_d16-Ritnh-elrerqKQi81FVKZ7kADljKacJcFpoolgaXhCE8yzNsqJMQmQViRWtlCZahykXkJcJA7pAl5Nub7twlfOyMa6EulYtdIOTsRAk5yGLAOUTtLSdcxa0HE9XdidjIkdD5V9D5WRo4F3sVwxFA9Uv68fBACAToBv6f2p-AStpiXg</recordid><startdate>20180601</startdate><enddate>20180601</enddate><creator>Kõressaar, Triinu</creator><creator>Lepamets, Maarja</creator><creator>Kaplinski, Lauris</creator><creator>Raime, Kairi</creator><creator>Andreson, Reidar</creator><creator>Remm, Maido</creator><general>Oxford University Press</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20180601</creationdate><title>Primer3_masker: integrating masking of template sequence with primer design software</title><author>Kõressaar, Triinu ; Lepamets, Maarja ; Kaplinski, Lauris ; Raime, Kairi ; Andreson, Reidar ; Remm, Maido</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c397t-dda528ee8446532e53bf0a4614690557677bc22227d01a3daf0ff76759e8c24e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kõressaar, Triinu</creatorcontrib><creatorcontrib>Lepamets, Maarja</creatorcontrib><creatorcontrib>Kaplinski, Lauris</creatorcontrib><creatorcontrib>Raime, Kairi</creatorcontrib><creatorcontrib>Andreson, Reidar</creatorcontrib><creatorcontrib>Remm, Maido</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Kõressaar, Triinu</au><au>Lepamets, Maarja</au><au>Kaplinski, Lauris</au><au>Raime, Kairi</au><au>Andreson, Reidar</au><au>Remm, Maido</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Primer3_masker: integrating masking of template sequence with primer design software</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2018-06-01</date><risdate>2018</risdate><volume>34</volume><issue>11</issue><spage>1937</spage><epage>1938</epage><pages>1937-1938</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract Summary Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the genomes contain a large number of repeat sequences and other regions unsuitable for amplification by PCR. We have developed a novel k-mer based masking method that uses a statistical model to detect and mask failure-prone regions on the DNA template prior to primer design. We implemented the software as a standalone software primer3_masker and integrated it into the primer design program Primer3. Availability and implementation The standalone version of primer3_masker is implemented in C. The source code is freely available at https://github.com/bioinfo-ut/primer3_masker/ (standalone version for Linux and macOS) and at https://github.com/primer3-org/primer3/ (integrated version). Primer3 web application that allows masking sequences of 196 animal and plant genomes is available at http://primer3.ut.ee/. Supplementary information Supplementary data are available at Bioinformatics online.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>29360956</pmid><doi>10.1093/bioinformatics/bty036</doi><tpages>2</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext_linktorsrc
identifier ISSN: 1367-4803
ispartof Bioinformatics, 2018-06, Vol.34 (11), p.1937-1938
issn 1367-4803
1460-2059
1367-4811
language eng
recordid cdi_proquest_miscellaneous_1990851999
source Oxford Journals Open Access Collection
title Primer3_masker: integrating masking of template sequence with primer design software
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-09T23%3A10%3A30IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_TOX&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Primer3_masker:%20integrating%20masking%20of%20template%20sequence%20with%20primer%20design%20software&rft.jtitle=Bioinformatics&rft.au=K%C3%B5ressaar,%20Triinu&rft.date=2018-06-01&rft.volume=34&rft.issue=11&rft.spage=1937&rft.epage=1938&rft.pages=1937-1938&rft.issn=1367-4803&rft.eissn=1460-2059&rft_id=info:doi/10.1093/bioinformatics/bty036&rft_dat=%3Cproquest_TOX%3E1990851999%3C/proquest_TOX%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1990851999&rft_id=info:pmid/29360956&rft_oup_id=10.1093/bioinformatics/bty036&rfr_iscdi=true