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Webtag: a new web tool providing tags/anchors for RT-PCR experiments with prokaryotes.

Pinto FL, Svensson H, Lindblad P - BMC Biotechnol. (2007)

Bottom Line: Webtag is a tool providing oligonucleotide sequences (usually called tags or anchors) that are absent from a specified genome.These tags/anchors can be appended to gene specific primers for reverse transcriptase polymerase chain reaction experiments, circumventing genomic DNA contamination.The use of a relational database, in conjunction with a series of scripts written in PHP and Perl, allows the user to rapidly obtain tags that are: 1) suitable for a specific organism, and 2) compatible with other oligonucleotides to be used in the experimental procedures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Photochemistry and Molecular Science, The Angström Laboratories, Uppsala University, Box 523, SE-75120, Uppsala, Sweden. fernando.lopespinto@fotomol.uu.se

ABSTRACT

Background: Webtag is a tool providing oligonucleotide sequences (usually called tags or anchors) that are absent from a specified genome. These tags/anchors can be appended to gene specific primers for reverse transcriptase polymerase chain reaction experiments, circumventing genomic DNA contamination.

Results: The use of a relational database, in conjunction with a series of scripts written in PHP and Perl, allows the user to rapidly obtain tags that are: 1) suitable for a specific organism, and 2) compatible with other oligonucleotides to be used in the experimental procedures.

Conclusion: This new web tool allows scientists to easily and rapidly obtain suitable tags for RT-PCR experiments, and is available at http://www.egs.uu.se/software/webtag/.

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Related in: MedlinePlus

Schematic describing tag generation, tag validation and database building processes.
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Figure 2: Schematic describing tag generation, tag validation and database building processes.

Mentions: The tags in the Webtag relational database were constructed as shown in Figure 2. Initially, all combinations of 5 bases long sequences containing the 4 bases A, T, C and G were filtered in order to select adequate "3'end regions". Briefly, this region should contain: a) a terminal G or C (to insure specific binding), b) between 2 and 3 G's or C's (for 3'end stability) and c) never more than 2 G's or C's in a row (to avoid false priming). The generation proceeded by adding more bases to selected 3'regions. During the construction of the "central region" di-nucleotide repeats and long runs of a single base were avoided. Finally, the "5'end region" was added. Just like for the "3'end region" the length is 5 bases, but the selection parameters were more relaxed (while maintaining binding stability at the 5'end).


Webtag: a new web tool providing tags/anchors for RT-PCR experiments with prokaryotes.

Pinto FL, Svensson H, Lindblad P - BMC Biotechnol. (2007)

Schematic describing tag generation, tag validation and database building processes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2147000&req=5

Figure 2: Schematic describing tag generation, tag validation and database building processes.
Mentions: The tags in the Webtag relational database were constructed as shown in Figure 2. Initially, all combinations of 5 bases long sequences containing the 4 bases A, T, C and G were filtered in order to select adequate "3'end regions". Briefly, this region should contain: a) a terminal G or C (to insure specific binding), b) between 2 and 3 G's or C's (for 3'end stability) and c) never more than 2 G's or C's in a row (to avoid false priming). The generation proceeded by adding more bases to selected 3'regions. During the construction of the "central region" di-nucleotide repeats and long runs of a single base were avoided. Finally, the "5'end region" was added. Just like for the "3'end region" the length is 5 bases, but the selection parameters were more relaxed (while maintaining binding stability at the 5'end).

Bottom Line: Webtag is a tool providing oligonucleotide sequences (usually called tags or anchors) that are absent from a specified genome.These tags/anchors can be appended to gene specific primers for reverse transcriptase polymerase chain reaction experiments, circumventing genomic DNA contamination.The use of a relational database, in conjunction with a series of scripts written in PHP and Perl, allows the user to rapidly obtain tags that are: 1) suitable for a specific organism, and 2) compatible with other oligonucleotides to be used in the experimental procedures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Photochemistry and Molecular Science, The Angström Laboratories, Uppsala University, Box 523, SE-75120, Uppsala, Sweden. fernando.lopespinto@fotomol.uu.se

ABSTRACT

Background: Webtag is a tool providing oligonucleotide sequences (usually called tags or anchors) that are absent from a specified genome. These tags/anchors can be appended to gene specific primers for reverse transcriptase polymerase chain reaction experiments, circumventing genomic DNA contamination.

Results: The use of a relational database, in conjunction with a series of scripts written in PHP and Perl, allows the user to rapidly obtain tags that are: 1) suitable for a specific organism, and 2) compatible with other oligonucleotides to be used in the experimental procedures.

Conclusion: This new web tool allows scientists to easily and rapidly obtain suitable tags for RT-PCR experiments, and is available at http://www.egs.uu.se/software/webtag/.

Show MeSH
Related in: MedlinePlus