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FOUNTAIN: a JAVA open-source package to assist large sequencing projects.

Buerstedde JM, Prill F - BMC Bioinformatics (2001)

Bottom Line: In addition, simple algorithms to cluster sequences and determine putative polymorphic positions are implemented.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cellular Immunology, Heinrich-Pette-Institute, Martinistr 52, 20251 Hamburg, Germany. buersted@genetics.hpi.uni-hamburg.de

ABSTRACT

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 http://genetics.hpi.uni-hamburg.de/FOUNTAIN.html. 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.

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The tables of the Polymorphism work package. Primary – foreign key relationships are indicated by lines between columns.
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Figure 5: The tables of the Polymorphism work package. Primary – foreign key relationships are indicated by lines between columns.

Mentions: The Polymorphism work package (Fig. 5) tries to define possible polymorphism or errors in the sequences. It includes all classes and sub packages of 'fountain.genetics.polymorphism'.


FOUNTAIN: a JAVA open-source package to assist large sequencing projects.

Buerstedde JM, Prill F - BMC Bioinformatics (2001)

The tables of the Polymorphism work package. Primary – foreign key relationships are indicated by lines between columns.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC57735&req=5

Figure 5: The tables of the Polymorphism work package. Primary – foreign key relationships are indicated by lines between columns.
Mentions: The Polymorphism work package (Fig. 5) tries to define possible polymorphism or errors in the sequences. It includes all classes and sub packages of 'fountain.genetics.polymorphism'.

Bottom Line: In addition, simple algorithms to cluster sequences and determine putative polymorphic positions are implemented.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cellular Immunology, Heinrich-Pette-Institute, Martinistr 52, 20251 Hamburg, Germany. buersted@genetics.hpi.uni-hamburg.de

ABSTRACT

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 http://genetics.hpi.uni-hamburg.de/FOUNTAIN.html. 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.

Show MeSH