KASpOD - a web service for highly specific and explorative oligonucleotide design

SUMMARY KASpOD is a web service dedicated to the design of signature sequences using a k-mer-based algorithm. Such highly specific and explorative oligonucleotides are then suitable for various goals, including Phylogenetic Oligonucleotide Arrays. AVAILABILITY http://g2im.u-clermont1.fr/kaspod. CONTACT eric.peyretaillade@udamail.fr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

[1]  Peter L. Williams,et al.  Skip the Alignment: Degenerate, Multiplex Primer and Probe Design Using K-mer Matching Instead of Alignments , 2012, PloS one.

[2]  Christopher Quince,et al.  The rational exploration of microbial diversity , 2008, The ISME Journal.

[3]  E. Dugat-Bony,et al.  Detecting unknown sequences with DNA microarrays: explorative probe design strategies. , 2012, Environmental microbiology.

[4]  M. David,et al.  In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes , 2012, Microbial biotechnology.

[5]  David R. C. Hill,et al.  GoArrays: highly dynamic and efficient microarray probe design , 2005, Bioinform..

[6]  Vincent Barra,et al.  PhylArray: phylogenetic probe design algorithm for microarray. , 2007, Bioinformatics.

[7]  Janet Kelso,et al.  PatMaN: rapid alignment of short sequences to large databases , 2008, Bioinform..

[8]  Carl Kingsford,et al.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..

[9]  Christian Grothoff,et al.  Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets , 2011, Bioinform..

[10]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[11]  Eric Peyretaillade,et al.  Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development , 2010, BMC Bioinformatics.

[12]  Thomas Rattei,et al.  probeCheck – a central resource for evaluating oligonucleotide probe coverage and specificity , 2008, Environmental microbiology.

[13]  Michael Wagner,et al.  Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions , 2007, Microbial Ecology.

[14]  Eric P. Nawrocki,et al.  An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.