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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

Screen shot from circumsporozoite protein (ACO49545.1), merozoite surface protein 1 (XP_001352170.1), and merozoite surface protein 9 (AAN36363.1) element repetitive search: (a) visualization of results through the jqGrid plugin: by clicking over the repetitive element the graphical view is opened; (b) repetitive elements are mapped and displayed graphically through JBrowse.
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fig4: Screen shot from circumsporozoite protein (ACO49545.1), merozoite surface protein 1 (XP_001352170.1), and merozoite surface protein 9 (AAN36363.1) element repetitive search: (a) visualization of results through the jqGrid plugin: by clicking over the repetitive element the graphical view is opened; (b) repetitive elements are mapped and displayed graphically through JBrowse.

Mentions: Table 3 presents the result of executing the circumsporozoite protein (ACO49545.1), merozoite surface protein 1 (XP_001352170.1), and merozoite surface protein 9 (AAN36363.1), in which the repetitive element PNAN (PRO-ASN-ALA-ASN) was identified in the circumsporozoite protein as in previous work [24]. In other proteins, repetitive elements have been identified with low repetition frequency. Figure 4 shows the result that is available to the user in the web environment: (A) visualization of results through the jqGrid plugin: clicking over the repetitive element opens the graphical view; (B) repetitive elements are mapped and displayed graphically through JBrowse. In the web environment an identification code is generated for each execution. The code can be used to review the result when necessary and it is still possible to receive a link with the code by email to notify the user.


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)

Screen shot from circumsporozoite protein (ACO49545.1), merozoite surface protein 1 (XP_001352170.1), and merozoite surface protein 9 (AAN36363.1) element repetitive search: (a) visualization of results through the jqGrid plugin: by clicking over the repetitive element the graphical view is opened; (b) repetitive elements are mapped and displayed graphically through JBrowse.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: Screen shot from circumsporozoite protein (ACO49545.1), merozoite surface protein 1 (XP_001352170.1), and merozoite surface protein 9 (AAN36363.1) element repetitive search: (a) visualization of results through the jqGrid plugin: by clicking over the repetitive element the graphical view is opened; (b) repetitive elements are mapped and displayed graphically through JBrowse.
Mentions: Table 3 presents the result of executing the circumsporozoite protein (ACO49545.1), merozoite surface protein 1 (XP_001352170.1), and merozoite surface protein 9 (AAN36363.1), in which the repetitive element PNAN (PRO-ASN-ALA-ASN) was identified in the circumsporozoite protein as in previous work [24]. In other proteins, repetitive elements have been identified with low repetition frequency. Figure 4 shows the result that is available to the user in the web environment: (A) visualization of results through the jqGrid plugin: clicking over the repetitive element opens the graphical view; (B) repetitive elements are mapped and displayed graphically through JBrowse. In the web environment an identification code is generated for each execution. The code can be used to review the result when necessary and it is still possible to receive a link with the code by email to notify the user.

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