BOND: Basic OligoNucleotide Design.

A coverage criterion for spaced seeds and its applications to support vector machine string kernels and k-mer distances. J Comput Biol (2014) 0.79

Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds. Algorithms Mol Biol (2017) 0.75

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

Basic local alignment search tool. J Mol Biol (1990) 659.07

PatternHunter: faster and more sensitive homology search. Bioinformatics (2002) 35.65

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A (1998) 24.28

Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol (2001) 14.57

Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res (2000) 6.20

Selection of optimal DNA oligos for gene expression arrays. Bioinformatics (2001) 5.19

OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res (2003) 4.64

Patternhunter II: highly sensitive and fast homology search. J Bioinform Comput Biol (2004) 4.24

Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol (2003) 4.24

PROBEmer: A web-based software tool for selecting optimal DNA oligos. Nucleic Acids Res (2003) 3.32

Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays. Nucleic Acids Res (2004) 2.91

Selection of oligonucleotide probes for protein coding sequences. Bioinformatics (2003) 2.89

OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes. Nucleic Acids Res (2005) 2.11

Picky: oligo microarray design for large genomes. Bioinformatics (2004) 1.83

Selecting signature oligonucleotides to identify organisms using DNA arrays. Bioinformatics (2002) 1.74

Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res (2005) 1.65

YODA: selecting signature oligonucleotides. Bioinformatics (2004) 1.59

ROSO: optimizing oligonucleotide probes for microarrays. Bioinformatics (2004) 1.53

A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization. BMC Genomics (2003) 1.51

GoArrays: highly dynamic and efficient microarray probe design. Bioinformatics (2004) 1.44

A unifying framework for seed sensitivity and its application to subset seeds. J Bioinform Comput Biol (2006) 1.39

Multiple spaced seeds for homology search. Bioinformatics (2007) 1.37

Oligodb--interactive design of oligo DNA for transcription profiling of human genes. Bioinformatics (2002) 1.36

FLASH: a fast look-up algorithm for string homology. Proc Int Conf Intell Syst Mol Biol (1993) 1.25

An evaluation of custom microarray applications: the oligonucleotide design challenge. Nucleic Acids Res (2009) 1.19

Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region. BMC Bioinformatics (2002) 0.99

MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays. BMC Bioinformatics (2005) 0.96

SpEED: fast computation of sensitive spaced seeds. Bioinformatics (2011) 0.92

Design of long oligonucleotide probes for functional gene detection in a microbial community. Bioinformatics (2005) 0.90

OligoFaktory: a visual tool for interactive oligonucleotide design. Bioinformatics (2005) 0.90

SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target Tm algorithm for reducing cross-hybridization in microarray gene expression experiments. Bioinformatics (2004) 0.83

Seeds for effective oligonucleotide design. BMC Genomics (2011) 0.78

Konnector v2.0: pseudo-long reads from paired-end sequencing data. BMC Med Genomics (2015) 0.80

Seeds for effective oligonucleotide design. BMC Genomics (2011) 0.78

Efficient algorithms for counting and reporting segregating sites in genomic sequences. J Comput Biol (2007) 0.75