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ProGeRF: proteome and genome repeat finder utilizing a fast parallel hash function.

Lopes Rda S, Moraes WJ, Rodrigues Tde S, Bartholomeu DC - Biomed Res Int (2015)

Bottom Line: ProGeRF is a web site for extracting repetitive regions from genome and proteome sequences.It was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse the results.ProGeRF (Proteome and Genome Repeat Finder) is freely available as a stand-alone program, from which the users can download the source code, and as a web tool.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Federal University of Mato Grosso, 78600-000 Barra do Garcas, MT, Brazil.

ABSTRACT
Repetitive element sequences are adjacent, repeating patterns, also called motifs, and can be of different lengths; repetitions can involve their exact or approximate copies. They have been widely used as molecular markers in population biology. Given the sizes of sequenced genomes, various bioinformatics tools have been developed for the extraction of repetitive elements from DNA sequences. However, currently available tools do not provide options for identifying repetitive elements in the genome or proteome, displaying a user-friendly web interface, and performing-exhaustive searches. ProGeRF is a web site for extracting repetitive regions from genome and proteome sequences. It was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse the results. ProGeRF (Proteome and Genome Repeat Finder) is freely available as a stand-alone program, from which the users can download the source code, and as a web tool. It was developed using the hash table approach to extract perfect and imperfect repetitive regions in a (multi)FASTA file, while allowing a linear time complexity.

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Related in: MedlinePlus

ProGeRF architecture. Structure of the tool both for the web environment and for the stand-alone mode. The dark blue rectangles with rounded corners represent interfaces with the system. The transparent rectangles with a blue background represent algorithms done in C or Perl. The process script receives data from the web environment, treats the data, saves them in a MySql database, and calls the repetition extract module.
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Related In: Results  -  Collection


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fig1: ProGeRF architecture. Structure of the tool both for the web environment and for the stand-alone mode. The dark blue rectangles with rounded corners represent interfaces with the system. The transparent rectangles with a blue background represent algorithms done in C or Perl. The process script receives data from the web environment, treats the data, saves them in a MySql database, and calls the repetition extract module.

Mentions: ProGeRF is available in two execution modes, as illustrated in Figure 1: as a stand-alone program, from which the users can download the source code, compile, and run in their machine in a Linux environment and as a web tool available at the web address http://64.79.105.19/ligp/. At this address, it is also possible to download the stand-alone version.


ProGeRF: proteome and genome repeat finder utilizing a fast parallel hash function.

Lopes Rda S, Moraes WJ, Rodrigues Tde S, Bartholomeu DC - Biomed Res Int (2015)

ProGeRF architecture. Structure of the tool both for the web environment and for the stand-alone mode. The dark blue rectangles with rounded corners represent interfaces with the system. The transparent rectangles with a blue background represent algorithms done in C or Perl. The process script receives data from the web environment, treats the data, saves them in a MySql database, and calls the repetition extract module.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4355816&req=5

fig1: ProGeRF architecture. Structure of the tool both for the web environment and for the stand-alone mode. The dark blue rectangles with rounded corners represent interfaces with the system. The transparent rectangles with a blue background represent algorithms done in C or Perl. The process script receives data from the web environment, treats the data, saves them in a MySql database, and calls the repetition extract module.
Mentions: ProGeRF is available in two execution modes, as illustrated in Figure 1: as a stand-alone program, from which the users can download the source code, compile, and run in their machine in a Linux environment and as a web tool available at the web address http://64.79.105.19/ligp/. At this address, it is also possible to download the stand-alone version.

Bottom Line: ProGeRF is a web site for extracting repetitive regions from genome and proteome sequences.It was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse the results.ProGeRF (Proteome and Genome Repeat Finder) is freely available as a stand-alone program, from which the users can download the source code, and as a web tool.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Federal University of Mato Grosso, 78600-000 Barra do Garcas, MT, Brazil.

ABSTRACT
Repetitive element sequences are adjacent, repeating patterns, also called motifs, and can be of different lengths; repetitions can involve their exact or approximate copies. They have been widely used as molecular markers in population biology. Given the sizes of sequenced genomes, various bioinformatics tools have been developed for the extraction of repetitive elements from DNA sequences. However, currently available tools do not provide options for identifying repetitive elements in the genome or proteome, displaying a user-friendly web interface, and performing-exhaustive searches. ProGeRF is a web site for extracting repetitive regions from genome and proteome sequences. It was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse the results. ProGeRF (Proteome and Genome Repeat Finder) is freely available as a stand-alone program, from which the users can download the source code, and as a web tool. It was developed using the hash table approach to extract perfect and imperfect repetitive regions in a (multi)FASTA file, while allowing a linear time complexity.

Show MeSH
Related in: MedlinePlus