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KASpOD specifications

Information


Unique identifier OMICS_09149
Name KASpOD
Alternative name K-mer based algorithm for high specific oligonucleotide design
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Two FASTA files: one containing the target group and the second with the non-target sequences
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Pierre Peyret <>

Information


Unique identifier OMICS_09149
Name KASpOD
Alternative name K-mer based algorithm for high specific oligonucleotide design
Interface Web user interface
Restrictions to use None
Input data Two FASTA files: one containing the target group and the second with the non-target sequences
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pierre Peyret <>

Publication for K-mer based algorithm for high specific oligonucleotide design

KASpOD in publications

 (7)
PMCID: 5870382
PMID: 29587880
DOI: 10.1186/s40168-018-0442-3

[…] database corresponding to all 16s rrna gene diversity was constructed from the embl []. a set of 28- to 50-mer degenerate probes (additional file : table s2) was designed from these databases using kaspod [] and phylarray [] software that enable the determination of degenerate explorative capture probes. a minimal probe set composed of 15 probes has been selected so that probes are distributed […]

PMCID: 5351058
PMID: 28292322
DOI: 10.1186/s40168-017-0251-0

[…] to the lina1, lina2, and lina3 types [], have been extracted from genbank (december 18, 2014). a set of four 80-mer degenerate non-overlapping probes was designed from these sequences using kaspod software [] that allows for the design of specific probes based on large sequence datasets (additional file : table s1). the four selected probes are distributed uniformly over the entire […]

PMCID: 5499648
PMID: 28338834
DOI: 10.1093/dnares/dsx002

[…] (denaturation: 94 °c for 30s; annealing: 55–68 °c for 30 s; extension: 72 °c for 30 s), followed by 30 cycles of regular pcr with annealing at 52 °c. specific 5′ and 3′ primers were defined using kaspod software., amplification products were analysed by electrophoresis on 1.5% agarose gels. bands of the expected sizes were excised and purified using the wizard sv gel and pcr clean-up system […]

PMCID: 4889952
PMID: 27105841
DOI: 10.1093/nar/gkw309

[…] variant-specific and explorative probes to provide comprehensive diversity. dedicated software has been developed to meet this specific need, such as phylarray (), metabolicdesign (), hispod () and kaspod (). therefore, hybridization capture for the exploration of metagenomic samples appears to be a particularly promising strategy with diverse applications., in the light of the studies […]

PMCID: 4589312
PMID: 26421846
DOI: 10.1371/journal.pone.0139075

[…] pcr (denaturation: 94°c for 30s; annealing: 68–55°c for 30s; extension: 72°c for 30s), followed by 30 cycles of regular pcr with annealing at 52°c. specific gene primers were defined using the kaspod software []., presence and size of the amplification products were determined by electrophoresis on 1.5% agarose gels. bands of the expected sizes were excised and purified using the wizard sv […]


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KASpOD institution(s)
Clermont Université, Université d’Auvergne, EA 4678 CIDAM; UMR CNRS 6023, Université Blaise Pascal, Clermont-Ferrand, France; Clermont Université, Université d’Auvergne, UFR Pharmacie, Clermont-Ferrand, France
KASpOD funding source(s)
This work was supported by Direction Générale de l’Armement (DGA).

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