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FOUNTAIN: A JAVA open-source package to assist large sequencing projects
BACKGROUND: 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 laboratori...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2001
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC57735/ https://www.ncbi.nlm.nih.gov/pubmed/11591214 http://dx.doi.org/10.1186/1471-2105-2-6 |
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author | Buerstedde, Jean-Marie Prill, Florian |
author_facet | Buerstedde, Jean-Marie Prill, Florian |
author_sort | Buerstedde, Jean-Marie |
collection | PubMed |
description | BACKGROUND: 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. RESULTS: We describe here a new program, named FOUNTAIN, for the management of large sequencing projects . 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. CONCLUSIONS: 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. |
format | Text |
id | pubmed-57735 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2001 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-577352001-10-09 FOUNTAIN: A JAVA open-source package to assist large sequencing projects Buerstedde, Jean-Marie Prill, Florian BMC Bioinformatics Methodology Article BACKGROUND: 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. RESULTS: We describe here a new program, named FOUNTAIN, for the management of large sequencing projects . 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. CONCLUSIONS: 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. BioMed Central 2001-09-21 /pmc/articles/PMC57735/ /pubmed/11591214 http://dx.doi.org/10.1186/1471-2105-2-6 Text en Copyright © 2001 Buerstedde and Prill; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. |
spellingShingle | Methodology Article Buerstedde, Jean-Marie Prill, Florian FOUNTAIN: A JAVA open-source package to assist large sequencing projects |
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 |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC57735/ https://www.ncbi.nlm.nih.gov/pubmed/11591214 http://dx.doi.org/10.1186/1471-2105-2-6 |
work_keys_str_mv | AT buersteddejeanmarie fountainajavaopensourcepackagetoassistlargesequencingprojects AT prillflorian fountainajavaopensourcepackagetoassistlargesequencingprojects |