OligoCalc pipeline

OligoCalc specifications

Information


Unique identifier OMICS_02351
Name OligoCalc
Alternative name Oligonucleotide properties Calculator
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Warren A. Kibbe <>

Publication for Oligonucleotide properties Calculator

OligoCalc IN pipelines

 (2)
2017
PMCID: 5729218
PMID: 29242834
DOI: 10.1128/mSphere.00488-17

[…] sequence contigs representing 3,842 fungal species., published and custom-designed primers (tables s1 and s2) were evaluated to identify pairs with melting temperature differences of <5°c using oligocalc (42). next, the primer pairs were scored for taxonomic coverage and amplicon size using the sis database with primerprospector (39). the amplicon range was chosen to specifically work […]

2013
PMCID: 3833222
PMID: 24136150
DOI: 10.1038/bjc.2013.637

[…] samples. primer pairs for pcr amplification and sequencing were designed using primer3 (http://frodo.wi.mit.edu/) to flank exons (supplementary materials). the sequences were then filtered using oligocalc software (kibbe, 2007) to avoid hairpin formation and ucsc in silico pcr software to ensure yield of a single product. dna from any ffpe sample in which a mutation was found was extracted […]

OligoCalc institution(s)
Robert H Lurie Comprehensive Cancer Center, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA

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