Loading…
BatchPrimer3: a high throughput web application for PCR and sequencing primer design
Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-...
Saved in:
Published in: | BMC bioinformatics 2008-05, Vol.9 (1), p.253-253, Article 253 |
---|---|
Main Authors: | , , , , , , , , |
Format: | Article |
Language: | English |
Subjects: | |
Citations: | Items that this one cites |
Online Access: | Get full text |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
cited_by | |
---|---|
cites | cdi_FETCH-LOGICAL-b567t-c63bb84ceef0d8c96aa98ad2899120a96252f02f5f11ce621e5822bd73730ad13 |
container_end_page | 253 |
container_issue | 1 |
container_start_page | 253 |
container_title | BMC bioinformatics |
container_volume | 9 |
creator | You, Frank M Huo, Naxin Gu, Yong Qiang Luo, Ming-Cheng Ma, Yaqin Hane, Dave Lazo, Gerard R Dvorak, Jan Anderson, Olin D |
description | Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded.
A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories.
BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at http://wheat.pw.usda.gov/demos/BatchPrimer3/. |
doi_str_mv | 10.1186/1471-2105-9-253 |
format | article |
fullrecord | <record><control><sourceid>proquest_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_8f4dea7181114869aea401093e95f671</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><doaj_id>oai_doaj_org_article_8f4dea7181114869aea401093e95f671</doaj_id><sourcerecordid>69246666</sourcerecordid><originalsourceid>FETCH-LOGICAL-b567t-c63bb84ceef0d8c96aa98ad2899120a96252f02f5f11ce621e5822bd73730ad13</originalsourceid><addsrcrecordid>eNqFkkFv1DAQhS0EomXhzA35xC3UYyeOzQGJrlqoVIkKlbM1cZzEVTYOdgLi35N0V6UrgfBlrJmnT09vhpDXwN4BKHkGeQkZB1ZkOuOFeEJOHzpPH_1PyIuU7hiDUrHiOTkBVQArJTslt-c42e4m-p2L4j1F2vm2o1MXw9x24zzRn66iOI69tzj5MNAmRHqz_UpxqGly32c3WD-0dLwn0Nol3w4vybMG--ReHeqGfLu8uN1-zq6_fLrafrzOqkKWU2alqCqVW-caViurJaJWWHOlNXCGWvKCN4w3RQNgneTgCsV5VZeiFAxrEBtytefWAe_MagHjLxPQm_tGiK3BOHnbO6OavHZYggKAXEmNDnMGTAuni0aWK-vDnjXO1c7V1g1TxP4IejwZfGfa8MPwXCixZL8h53tA5cM_AMcTG3Zm3ZBZN2S0WRgL5O3BRQxLtmkyO5-s63scXJiTkZrncnn_FS5MrgTji_BsL7QxpBRd8-AImFlv6C8e3jxO4o_-cDTiN6Jpwck</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>21028302</pqid></control><display><type>article</type><title>BatchPrimer3: a high throughput web application for PCR and sequencing primer design</title><source>PubMed Central Free</source><creator>You, Frank M ; Huo, Naxin ; Gu, Yong Qiang ; Luo, Ming-Cheng ; Ma, Yaqin ; Hane, Dave ; Lazo, Gerard R ; Dvorak, Jan ; Anderson, Olin D</creator><creatorcontrib>You, Frank M ; Huo, Naxin ; Gu, Yong Qiang ; Luo, Ming-Cheng ; Ma, Yaqin ; Hane, Dave ; Lazo, Gerard R ; Dvorak, Jan ; Anderson, Olin D</creatorcontrib><description>Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded.
A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories.
BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at http://wheat.pw.usda.gov/demos/BatchPrimer3/.</description><identifier>ISSN: 1471-2105</identifier><identifier>EISSN: 1471-2105</identifier><identifier>DOI: 10.1186/1471-2105-9-253</identifier><identifier>PMID: 18510760</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Algorithms ; Base Sequence ; Brachypodium ; DNA Primers - genetics ; Genetic Markers - genetics ; Internet ; Microsatellite Repeats - genetics ; Molecular Sequence Data ; Polymerase Chain Reaction - methods ; Polymorphism, Single Nucleotide - genetics ; Sequence Analysis, DNA - methods ; Software ; Triticum aestivum</subject><ispartof>BMC bioinformatics, 2008-05, Vol.9 (1), p.253-253, Article 253</ispartof><rights>Copyright © 2008 You et al; licensee BioMed Central Ltd. 2008 You et al; licensee BioMed Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-b567t-c63bb84ceef0d8c96aa98ad2899120a96252f02f5f11ce621e5822bd73730ad13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2438325/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2438325/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18510760$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>You, Frank M</creatorcontrib><creatorcontrib>Huo, Naxin</creatorcontrib><creatorcontrib>Gu, Yong Qiang</creatorcontrib><creatorcontrib>Luo, Ming-Cheng</creatorcontrib><creatorcontrib>Ma, Yaqin</creatorcontrib><creatorcontrib>Hane, Dave</creatorcontrib><creatorcontrib>Lazo, Gerard R</creatorcontrib><creatorcontrib>Dvorak, Jan</creatorcontrib><creatorcontrib>Anderson, Olin D</creatorcontrib><title>BatchPrimer3: a high throughput web application for PCR and sequencing primer design</title><title>BMC bioinformatics</title><addtitle>BMC Bioinformatics</addtitle><description>Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded.
A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories.
BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at http://wheat.pw.usda.gov/demos/BatchPrimer3/.</description><subject>Algorithms</subject><subject>Base Sequence</subject><subject>Brachypodium</subject><subject>DNA Primers - genetics</subject><subject>Genetic Markers - genetics</subject><subject>Internet</subject><subject>Microsatellite Repeats - genetics</subject><subject>Molecular Sequence Data</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Software</subject><subject>Triticum aestivum</subject><issn>1471-2105</issn><issn>1471-2105</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>DOA</sourceid><recordid>eNqFkkFv1DAQhS0EomXhzA35xC3UYyeOzQGJrlqoVIkKlbM1cZzEVTYOdgLi35N0V6UrgfBlrJmnT09vhpDXwN4BKHkGeQkZB1ZkOuOFeEJOHzpPH_1PyIuU7hiDUrHiOTkBVQArJTslt-c42e4m-p2L4j1F2vm2o1MXw9x24zzRn66iOI69tzj5MNAmRHqz_UpxqGly32c3WD-0dLwn0Nol3w4vybMG--ReHeqGfLu8uN1-zq6_fLrafrzOqkKWU2alqCqVW-caViurJaJWWHOlNXCGWvKCN4w3RQNgneTgCsV5VZeiFAxrEBtytefWAe_MagHjLxPQm_tGiK3BOHnbO6OavHZYggKAXEmNDnMGTAuni0aWK-vDnjXO1c7V1g1TxP4IejwZfGfa8MPwXCixZL8h53tA5cM_AMcTG3Zm3ZBZN2S0WRgL5O3BRQxLtmkyO5-s63scXJiTkZrncnn_FS5MrgTji_BsL7QxpBRd8-AImFlv6C8e3jxO4o_-cDTiN6Jpwck</recordid><startdate>20080529</startdate><enddate>20080529</enddate><creator>You, Frank M</creator><creator>Huo, Naxin</creator><creator>Gu, Yong Qiang</creator><creator>Luo, Ming-Cheng</creator><creator>Ma, Yaqin</creator><creator>Hane, Dave</creator><creator>Lazo, Gerard R</creator><creator>Dvorak, Jan</creator><creator>Anderson, Olin D</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><general>BMC</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20080529</creationdate><title>BatchPrimer3: a high throughput web application for PCR and sequencing primer design</title><author>You, Frank M ; Huo, Naxin ; Gu, Yong Qiang ; Luo, Ming-Cheng ; Ma, Yaqin ; Hane, Dave ; Lazo, Gerard R ; Dvorak, Jan ; Anderson, Olin D</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b567t-c63bb84ceef0d8c96aa98ad2899120a96252f02f5f11ce621e5822bd73730ad13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Algorithms</topic><topic>Base Sequence</topic><topic>Brachypodium</topic><topic>DNA Primers - genetics</topic><topic>Genetic Markers - genetics</topic><topic>Internet</topic><topic>Microsatellite Repeats - genetics</topic><topic>Molecular Sequence Data</topic><topic>Polymerase Chain Reaction - methods</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Software</topic><topic>Triticum aestivum</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>You, Frank M</creatorcontrib><creatorcontrib>Huo, Naxin</creatorcontrib><creatorcontrib>Gu, Yong Qiang</creatorcontrib><creatorcontrib>Luo, Ming-Cheng</creatorcontrib><creatorcontrib>Ma, Yaqin</creatorcontrib><creatorcontrib>Hane, Dave</creatorcontrib><creatorcontrib>Lazo, Gerard R</creatorcontrib><creatorcontrib>Dvorak, Jan</creatorcontrib><creatorcontrib>Anderson, Olin D</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>BMC bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>You, Frank M</au><au>Huo, Naxin</au><au>Gu, Yong Qiang</au><au>Luo, Ming-Cheng</au><au>Ma, Yaqin</au><au>Hane, Dave</au><au>Lazo, Gerard R</au><au>Dvorak, Jan</au><au>Anderson, Olin D</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>BatchPrimer3: a high throughput web application for PCR and sequencing primer design</atitle><jtitle>BMC bioinformatics</jtitle><addtitle>BMC Bioinformatics</addtitle><date>2008-05-29</date><risdate>2008</risdate><volume>9</volume><issue>1</issue><spage>253</spage><epage>253</epage><pages>253-253</pages><artnum>253</artnum><issn>1471-2105</issn><eissn>1471-2105</eissn><abstract>Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded.
A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories.
BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at http://wheat.pw.usda.gov/demos/BatchPrimer3/.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>18510760</pmid><doi>10.1186/1471-2105-9-253</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 1471-2105 |
ispartof | BMC bioinformatics, 2008-05, Vol.9 (1), p.253-253, Article 253 |
issn | 1471-2105 1471-2105 |
language | eng |
recordid | cdi_doaj_primary_oai_doaj_org_article_8f4dea7181114869aea401093e95f671 |
source | PubMed Central Free |
subjects | Algorithms Base Sequence Brachypodium DNA Primers - genetics Genetic Markers - genetics Internet Microsatellite Repeats - genetics Molecular Sequence Data Polymerase Chain Reaction - methods Polymorphism, Single Nucleotide - genetics Sequence Analysis, DNA - methods Software Triticum aestivum |
title | BatchPrimer3: a high throughput web application for PCR and sequencing primer design |
url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T17%3A35%3A52IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=BatchPrimer3:%20a%20high%20throughput%20web%20application%20for%20PCR%20and%20sequencing%20primer%20design&rft.jtitle=BMC%20bioinformatics&rft.au=You,%20Frank%20M&rft.date=2008-05-29&rft.volume=9&rft.issue=1&rft.spage=253&rft.epage=253&rft.pages=253-253&rft.artnum=253&rft.issn=1471-2105&rft.eissn=1471-2105&rft_id=info:doi/10.1186/1471-2105-9-253&rft_dat=%3Cproquest_doaj_%3E69246666%3C/proquest_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-b567t-c63bb84ceef0d8c96aa98ad2899120a96252f02f5f11ce621e5822bd73730ad13%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=21028302&rft_id=info:pmid/18510760&rfr_iscdi=true |