FOUNTAIN: A JAVA open-source package to assist large sequencing projects
<p>Abstract</p> <p>Background</p> <p>Better automation, lower cost per reaction and a heightened interest in comparative genomics has led to a dramatic increase in DNA sequencing activities. Although the large sequencing projects of specialized centers are supported by...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2001-09-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/2/6 |
| _version_ | 1811287455908757504 |
|---|---|
| author | Prill Florian Buerstedde Jean-Marie |
| author_facet | Prill Florian Buerstedde Jean-Marie |
| author_sort | Prill Florian |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Better automation, lower cost per reaction and a heightened interest in comparative genomics has led to a dramatic increase in DNA sequencing activities. Although the large sequencing projects of specialized centers are supported by in-house bioinformatics groups, many smaller laboratories face difficulties managing the appropriate processing and storage of their sequencing output. The challenges include documentation of clones, templates and sequencing reactions, and the storage, annotation and analysis of the large number of generated sequences.</p> <p>Results</p> <p>We describe here a new program, named FOUNTAIN, for the management of large sequencing projects <url>http://genetics.hpi.uni-hamburg.de/FOUNTAIN.html</url>. FOUNTAIN uses the JAVA computer language and data storage in a relational database. Starting with a collection of sequencing objects (clones), the program generates and stores information related to the different stages of the sequencing project using a web browser interface for user input. The generated sequences are subsequently imported and annotated based on BLAST searches against the public databases. In addition, simple algorithms to cluster sequences and determine putative polymorphic positions are implemented.</p> <p>Conclusions</p> <p>A simple, but flexible and scalable software package is presented to facilitate data generation and storage for large sequencing projects. Open source and largely platform and database independent, we wish FOUNTAIN to be improved and extended in a community effort.</p> |
| first_indexed | 2024-04-13T03:18:39Z |
| format | Article |
| id | doaj.art-a27a443aa6424494b496dd5063bf2403 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T03:18:39Z |
| publishDate | 2001-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-a27a443aa6424494b496dd5063bf24032022-12-22T03:04:50ZengBMCBMC Bioinformatics1471-21052001-09-0121610.1186/1471-2105-2-6FOUNTAIN: A JAVA open-source package to assist large sequencing projectsPrill FlorianBuerstedde Jean-Marie<p>Abstract</p> <p>Background</p> <p>Better automation, lower cost per reaction and a heightened interest in comparative genomics has led to a dramatic increase in DNA sequencing activities. Although the large sequencing projects of specialized centers are supported by in-house bioinformatics groups, many smaller laboratories face difficulties managing the appropriate processing and storage of their sequencing output. The challenges include documentation of clones, templates and sequencing reactions, and the storage, annotation and analysis of the large number of generated sequences.</p> <p>Results</p> <p>We describe here a new program, named FOUNTAIN, for the management of large sequencing projects <url>http://genetics.hpi.uni-hamburg.de/FOUNTAIN.html</url>. FOUNTAIN uses the JAVA computer language and data storage in a relational database. Starting with a collection of sequencing objects (clones), the program generates and stores information related to the different stages of the sequencing project using a web browser interface for user input. The generated sequences are subsequently imported and annotated based on BLAST searches against the public databases. In addition, simple algorithms to cluster sequences and determine putative polymorphic positions are implemented.</p> <p>Conclusions</p> <p>A simple, but flexible and scalable software package is presented to facilitate data generation and storage for large sequencing projects. Open source and largely platform and database independent, we wish FOUNTAIN to be improved and extended in a community effort.</p>http://www.biomedcentral.com/1471-2105/2/6 |
| spellingShingle | Prill Florian Buerstedde Jean-Marie FOUNTAIN: A JAVA open-source package to assist large sequencing projects BMC Bioinformatics |
| title | FOUNTAIN: A JAVA open-source package to assist large sequencing projects |
| title_full | FOUNTAIN: A JAVA open-source package to assist large sequencing projects |
| title_fullStr | FOUNTAIN: A JAVA open-source package to assist large sequencing projects |
| title_full_unstemmed | FOUNTAIN: A JAVA open-source package to assist large sequencing projects |
| title_short | FOUNTAIN: A JAVA open-source package to assist large sequencing projects |
| title_sort | fountain a java open source package to assist large sequencing projects |
| url | http://www.biomedcentral.com/1471-2105/2/6 |
| work_keys_str_mv | AT prillflorian fountainajavaopensourcepackagetoassistlargesequencingprojects AT buersteddejeanmarie fountainajavaopensourcepackagetoassistlargesequencingprojects |