JDotter: a Java interface to multiple dotplots generated by dotter

Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client–server application and can send new sequences to the Dotter program for alignment as w...

Full description

Saved in:
Bibliographic Details
Published in:Bioinformatics 2004-01, Vol.20 (2), p.279-281
Main Authors: Brodie, Ryan, Roper, Rachel L., Upton, Chris
Format: Article
Language:English
Subjects:
Biological and medical sciences
Computer Graphics
Database Management Systems
Databases, Nucleic Acid
Fundamental and applied biological sciences. Psychology
General aspects
Hypermedia
Information Storage and Retrieval - methods
Internet
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Software
Systems Integration
User-Computer Interface
Citations: Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c544t-672c9a44203f03c62a94c66b2ba3b12ad3e03a2d7a5254562edd46ba086ba3803
cites
container_end_page 281
container_issue 2
container_start_page 279
container_title Bioinformatics
container_volume 20
creator Brodie, Ryan
Roper, Rachel L.
Upton, Chris
description Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client–server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization. Availability: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. Supplementary information: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.
doi_str_mv 10.1093/bioinformatics/btg406
format article
fullrecord <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_80112711</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>530768191</sourcerecordid><originalsourceid>FETCH-LOGICAL-c544t-672c9a44203f03c62a94c66b2ba3b12ad3e03a2d7a5254562edd46ba086ba3803</originalsourceid><addsrcrecordid>eNqF0Utv1DAQAGALgWgp_ARQhAS3tLbHj4RbW2jLaiWEBAhxsSaOU7kk8WI7Ff33eLWrVnDh4uc348cQ8pLRY0ZbOOl88PMQ4oTZ23TS5WtB1SNyyISiNaeyfVzGoHQtGgoH5FlKN5RKJoR4Sg6Y0CCAwyE5W70PObv4rsJqhbdY-bnMBrSuyqGaljH7zeiqPuTNGHKqrt3sImbXV93ddrXg5-TJgGNyL_b9Efl68eHL-VW9_nT58fx0XVspRK6V5rZFITiFgYJVHFthlep4h9Axjj04Csh7jZJLIRV3fS9Uh7QpDZRHHJG3u7ybGH4tLmUz-WTdOOLswpJMQxnjmrH_QtZyoEq1Bb7-B96EJc7lEcU0SknRQEFyh2wMKUU3mE30E8Y7w6jZlsL8XQqzK0WJe7VPvnST6x-i9n9fwJs9wGRxHCLO1qcHV05nWmxvWe-cT9n9vt_H-NMoDVqaq-8_zHqlv8HZJTef4Q_g96S_</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>198665483</pqid></control><display><type>article</type><title>JDotter: a Java interface to multiple dotplots generated by dotter</title><source>Open Access: Oxford University Press Open Journals</source><creator>Brodie, Ryan ; Roper, Rachel L. ; Upton, Chris</creator><creatorcontrib>Brodie, Ryan ; Roper, Rachel L. ; Upton, Chris</creatorcontrib><description>Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client–server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization. Availability: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. Supplementary information: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btg406</identifier><identifier>PMID: 14734323</identifier><identifier>CODEN: BOINFP</identifier><language>eng</language><publisher>Oxford: Oxford University Press</publisher><subject>Biological and medical sciences ; Computer Graphics ; Database Management Systems ; Databases, Nucleic Acid ; Fundamental and applied biological sciences. Psychology ; General aspects ; Hypermedia ; Information Storage and Retrieval - methods ; Internet ; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) ; Sequence Alignment - methods ; Sequence Analysis, DNA - methods ; Software ; Systems Integration ; User-Computer Interface</subject><ispartof>Bioinformatics, 2004-01, Vol.20 (2), p.279-281</ispartof><rights>2004 INIST-CNRS</rights><rights>Copyright Oxford Publishing Limited(England) Jan 22 2004</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c544t-672c9a44203f03c62a94c66b2ba3b12ad3e03a2d7a5254562edd46ba086ba3803</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&amp;idt=15481749$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/14734323$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Brodie, Ryan</creatorcontrib><creatorcontrib>Roper, Rachel L.</creatorcontrib><creatorcontrib>Upton, Chris</creatorcontrib><title>JDotter: a Java interface to multiple dotplots generated by dotter</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client–server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization. Availability: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. Supplementary information: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.</description><subject>Biological and medical sciences</subject><subject>Computer Graphics</subject><subject>Database Management Systems</subject><subject>Databases, Nucleic Acid</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General aspects</subject><subject>Hypermedia</subject><subject>Information Storage and Retrieval - methods</subject><subject>Internet</subject><subject>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</subject><subject>Sequence Alignment - methods</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Software</subject><subject>Systems Integration</subject><subject>User-Computer Interface</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><recordid>eNqF0Utv1DAQAGALgWgp_ARQhAS3tLbHj4RbW2jLaiWEBAhxsSaOU7kk8WI7Ff33eLWrVnDh4uc348cQ8pLRY0ZbOOl88PMQ4oTZ23TS5WtB1SNyyISiNaeyfVzGoHQtGgoH5FlKN5RKJoR4Sg6Y0CCAwyE5W70PObv4rsJqhbdY-bnMBrSuyqGaljH7zeiqPuTNGHKqrt3sImbXV93ddrXg5-TJgGNyL_b9Efl68eHL-VW9_nT58fx0XVspRK6V5rZFITiFgYJVHFthlep4h9Axjj04Csh7jZJLIRV3fS9Uh7QpDZRHHJG3u7ybGH4tLmUz-WTdOOLswpJMQxnjmrH_QtZyoEq1Bb7-B96EJc7lEcU0SknRQEFyh2wMKUU3mE30E8Y7w6jZlsL8XQqzK0WJe7VPvnST6x-i9n9fwJs9wGRxHCLO1qcHV05nWmxvWe-cT9n9vt_H-NMoDVqaq-8_zHqlv8HZJTef4Q_g96S_</recordid><startdate>20040122</startdate><enddate>20040122</enddate><creator>Brodie, Ryan</creator><creator>Roper, Rachel L.</creator><creator>Upton, Chris</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>BSCLL</scope><scope>IQODW</scope><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>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7TM</scope><scope>7TO</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9.</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>20040122</creationdate><title>JDotter: a Java interface to multiple dotplots generated by dotter</title><author>Brodie, Ryan ; Roper, Rachel L. ; Upton, Chris</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c544t-672c9a44203f03c62a94c66b2ba3b12ad3e03a2d7a5254562edd46ba086ba3803</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Biological and medical sciences</topic><topic>Computer Graphics</topic><topic>Database Management Systems</topic><topic>Databases, Nucleic Acid</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General aspects</topic><topic>Hypermedia</topic><topic>Information Storage and Retrieval - methods</topic><topic>Internet</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</topic><topic>Sequence Alignment - methods</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Software</topic><topic>Systems Integration</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Brodie, Ryan</creatorcontrib><creatorcontrib>Roper, Rachel L.</creatorcontrib><creatorcontrib>Upton, Chris</creatorcontrib><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics &amp; Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical &amp; Transportation Engineering Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>ANTE: Abstracts in New Technology &amp; Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts – Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Brodie, Ryan</au><au>Roper, Rachel L.</au><au>Upton, Chris</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>JDotter: a Java interface to multiple dotplots generated by dotter</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2004-01-22</date><risdate>2004</risdate><volume>20</volume><issue>2</issue><spage>279</spage><epage>281</epage><pages>279-281</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><coden>BOINFP</coden><abstract>Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client–server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization. Availability: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. Supplementary information: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.</abstract><cop>Oxford</cop><pub>Oxford University Press</pub><pmid>14734323</pmid><doi>10.1093/bioinformatics/btg406</doi><tpages>3</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1367-4803
ispartof Bioinformatics, 2004-01, Vol.20 (2), p.279-281
issn 1367-4803
1460-2059
1367-4811
language eng
recordid cdi_proquest_miscellaneous_80112711
source Open Access: Oxford University Press Open Journals
subjects Biological and medical sciences
Computer Graphics
Database Management Systems
Databases, Nucleic Acid
Fundamental and applied biological sciences. Psychology
General aspects
Hypermedia
Information Storage and Retrieval - methods
Internet
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Software
Systems Integration
User-Computer Interface
title JDotter: a Java interface to multiple dotplots generated by dotter
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-26T21%3A35%3A53IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=JDotter:%20a%20Java%20interface%20to%20multiple%20dotplots%20generated%20by%20dotter&rft.jtitle=Bioinformatics&rft.au=Brodie,%20Ryan&rft.date=2004-01-22&rft.volume=20&rft.issue=2&rft.spage=279&rft.epage=281&rft.pages=279-281&rft.issn=1367-4803&rft.eissn=1460-2059&rft.coden=BOINFP&rft_id=info:doi/10.1093/bioinformatics/btg406&rft_dat=%3Cproquest_cross%3E530768191%3C/proquest_cross%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c544t-672c9a44203f03c62a94c66b2ba3b12ad3e03a2d7a5254562edd46ba086ba3803%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=198665483&rft_id=info:pmid/14734323&rfr_iscdi=true