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

Versioning


No version available

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 citation

library_books

Gene Capture Coupled to High Throughput Sequencing as a Strategy for Targeted Metagenome Exploration

2013
PMCID: 3628448
PMID: 23364577
DOI: 10.1093/dnares/dst001

[…] ed genes such as the 16S rRNA biomarker. The main limitation is the design of high quality probes sets to expect a full coverage of 16S rDNA sequences as complete as possible. New algorithms, such as KASpOD, can be used to design highly specific and explorative probes (i.e. targeting sequences not already included in databases) based on oligonucleotide k-mer signatures. These probe designs would b […]

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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