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RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences.

Sperber G, Lövgren A, Eriksson NE, Benachenhou F, Blomberg J - BMC Bioinformatics (2009)

Bottom Line: A better understanding of structure and function of these sequences can have profound biological and medical consequences.A "light" version of ReTe, (RetroTector online; ROL) which does not require specific installation procedures is provided, via the World Wide Web.A detailed analysis of any retroviral sequences found in the submitted sequence is graphically presented, exportable in standard formats.

View Article: PubMed Central - HTML - PubMed

Affiliation: Physiology unit, Department of Neuroscience, Box 593, Uppsala, Sweden. goran.sperber@neuro.uu.se

ABSTRACT

Background: The rapid accumulation of genomic information in databases necessitates rapid and specific algorithms for extracting biologically meaningful information. More or less complete retroviral sequences, also called proviral or endogenous retroviral sequences; ERVs, constitutes at least 5% of vertebrate genomes. After infecting the host, these retroviruses have integrated in germ line cells, and have then been carried in genomes for at least several 100 million years. A better understanding of structure and function of these sequences can have profound biological and medical consequences.

Methods: RetroTector (ReTe) is a platform-independent Java program for identification and characterization of proviral sequences in vertebrate genomes. The full ReTe requires a local installation with a MySQL database. Although not overly complicated, the installation may take some time. A "light" version of ReTe, (RetroTector online; ROL) which does not require specific installation procedures is provided, via the World Wide Web.

Result: ROL http://www.fysiologi.neuro.uu.se/jbgs/ was implemented under the Batchelor web interface (A Lövgren et al). It allows both GenBank accession number, file and FASTA cut-and-paste admission of sequences (5 to 10,000 kilobases). Up to ten submissions can be done simultaneously, allowing batch analysis of

Discussion: Proviral sequences can be hard to recognize, especially if the integration occurred many million years ago. Precise delineation of LTR, gag, pro, pol and env can be difficult, requiring manual work. ROL is a way of simplifying these tasks.

Conclusion: ROL provides 1. annotation and presentation of known retroviral sequences, 2. detection of proviral chains in unknown genomic sequences, with up to 100 Mbase per submission.

Show MeSH
User interface of RetroTector online. FASTA formatted sequences, each up to 10 Mbases long, can be entered as file, by cut-and-paste, and by GenBank accession number. Up to ten sequences can be entered at the same time.
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Related In: Results  -  Collection

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Figure 1: User interface of RetroTector online. FASTA formatted sequences, each up to 10 Mbases long, can be entered as file, by cut-and-paste, and by GenBank accession number. Up to ten sequences can be entered at the same time.

Mentions: The ROL implementation , under the Batchelor web interface, allows both GenBank accession number, file and FASTA cut-and-paste admission of sequences (5 to 1000 000 kilobases) (Figure 1). Up to ten submissions can be done simultaneously. Thus, a batch analysis of <= 100 Megabases can be specified in one instance. Jobs are shown in an IP-number specific list. Results are downloadable as text files. The text files derive from 100 000 base chunks. Names of chunks which contain one or several retroviral chains detected by ReTe are shown in bold face. Each retrovirus-positive chunk can be inspected by means of the stand-alone program, RetroTectorViewer.jar, which has the full graphical capabilities of the basic ReTe program. It can export in EPS, PDF and JPG formats. Thus, a detailed analysis of any retroviral sequences found in the submitted sequence is graphically presented. With the current server, a complete analysis of a 1 Megabase sequence is complete in under 10 minutes. It is possible to mask nonretroviral repetitive sequences in the submitted sequence before analysis, using host genome specific "brooms". This increases the specificity of the analysis.


RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences.

Sperber G, Lövgren A, Eriksson NE, Benachenhou F, Blomberg J - BMC Bioinformatics (2009)

User interface of RetroTector online. FASTA formatted sequences, each up to 10 Mbases long, can be entered as file, by cut-and-paste, and by GenBank accession number. Up to ten sequences can be entered at the same time.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697651&req=5

Figure 1: User interface of RetroTector online. FASTA formatted sequences, each up to 10 Mbases long, can be entered as file, by cut-and-paste, and by GenBank accession number. Up to ten sequences can be entered at the same time.
Mentions: The ROL implementation , under the Batchelor web interface, allows both GenBank accession number, file and FASTA cut-and-paste admission of sequences (5 to 1000 000 kilobases) (Figure 1). Up to ten submissions can be done simultaneously. Thus, a batch analysis of <= 100 Megabases can be specified in one instance. Jobs are shown in an IP-number specific list. Results are downloadable as text files. The text files derive from 100 000 base chunks. Names of chunks which contain one or several retroviral chains detected by ReTe are shown in bold face. Each retrovirus-positive chunk can be inspected by means of the stand-alone program, RetroTectorViewer.jar, which has the full graphical capabilities of the basic ReTe program. It can export in EPS, PDF and JPG formats. Thus, a detailed analysis of any retroviral sequences found in the submitted sequence is graphically presented. With the current server, a complete analysis of a 1 Megabase sequence is complete in under 10 minutes. It is possible to mask nonretroviral repetitive sequences in the submitted sequence before analysis, using host genome specific "brooms". This increases the specificity of the analysis.

Bottom Line: A better understanding of structure and function of these sequences can have profound biological and medical consequences.A "light" version of ReTe, (RetroTector online; ROL) which does not require specific installation procedures is provided, via the World Wide Web.A detailed analysis of any retroviral sequences found in the submitted sequence is graphically presented, exportable in standard formats.

View Article: PubMed Central - HTML - PubMed

Affiliation: Physiology unit, Department of Neuroscience, Box 593, Uppsala, Sweden. goran.sperber@neuro.uu.se

ABSTRACT

Background: The rapid accumulation of genomic information in databases necessitates rapid and specific algorithms for extracting biologically meaningful information. More or less complete retroviral sequences, also called proviral or endogenous retroviral sequences; ERVs, constitutes at least 5% of vertebrate genomes. After infecting the host, these retroviruses have integrated in germ line cells, and have then been carried in genomes for at least several 100 million years. A better understanding of structure and function of these sequences can have profound biological and medical consequences.

Methods: RetroTector (ReTe) is a platform-independent Java program for identification and characterization of proviral sequences in vertebrate genomes. The full ReTe requires a local installation with a MySQL database. Although not overly complicated, the installation may take some time. A "light" version of ReTe, (RetroTector online; ROL) which does not require specific installation procedures is provided, via the World Wide Web.

Result: ROL http://www.fysiologi.neuro.uu.se/jbgs/ was implemented under the Batchelor web interface (A Lövgren et al). It allows both GenBank accession number, file and FASTA cut-and-paste admission of sequences (5 to 10,000 kilobases). Up to ten submissions can be done simultaneously, allowing batch analysis of

Discussion: Proviral sequences can be hard to recognize, especially if the integration occurred many million years ago. Precise delineation of LTR, gag, pro, pol and env can be difficult, requiring manual work. ROL is a way of simplifying these tasks.

Conclusion: ROL provides 1. annotation and presentation of known retroviral sequences, 2. detection of proviral chains in unknown genomic sequences, with up to 100 Mbase per submission.

Show MeSH