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OligoPicker specifications

Information


Unique identifier OMICS_00830
Name OligoPicker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for OligoPicker

OligoPicker in publications

 (9)
PMCID: 3564981
PMID: 23390597
DOI: 10.1534/g3.112.004739

[…] including the insertion when present and flanking sequence centered on the middle of the indel., from the resulting sequence files, we selected 70-bp subsequences to be potential oligos by using oligopicker 2.3.2 (). oligo sequences were then trimmed from the 5′ end so that they would require no more than 180 synthesis cycles according to the roche nimblegen protocol. we then removed […]

PMCID: 3082872
PMID: 21149258
DOI: 10.1093/nar/gkq1242

[…] each end. sixty nucleotide long, negative control probes were created by generating random sequences with a 50% gc content and selecting those with low cross-reactivity against e. coli probes using oligopicker (). the final array design contained 231 984 e. coli probes, 6415 duplicate e. coli probes and 3000 random probes. probe sequences were submitted to agilent technologies (palo alto, ca, […]

PMCID: 3017858
PMID: 20964857
DOI: 10.1186/1471-2164-11-591

[…] sequence database. annotations were obtained manually from the most abundant function assigned to respective genomic regions. new amr-specific capture probes were designed by the programme oligopicker []. probe uniqueness was validated against the gdna of reference strains with blast []., samples of gdna extracted from representative strains of various enterobacterial pathogroups […]

PMCID: 2913925
PMID: 20626891
DOI: 10.1186/1756-0500-3-192

[…] in both possible transcript directions. afters the second blast procedure, in which the tc probes were aligned against the subsequences (figure ), 5,299 subsequences remained to be designed., oligopicker [] has been used to design up to 5 probes per sequence with a 3' sequence preference. a probe is considered to cross-hybridize, if it contains a stretch of 16 nucleotides […]

PMCID: 2267714
PMID: 18221507
DOI: 10.1186/1471-2164-9-38

[…] of selected genes has been obtained and deposited in a locally installed database base []., for each of the selected 1632 genes, a single 5'-aminomodified 40-mer oligonucleotide was designed using oligopicker software []. blast searches were performed with each candidate probe to exclude possibility of cross hybridization with homologous genes prior to the synthesis of oligonucleotide probes. […]


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OligoPicker institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Kgs, Lyngby, Denmark

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