OligoCalc: an online oligonucleotide properties calculator.
Reads0
Chats0
TLDR
OligoCalc incorporates three common methods for calculating oligonucleotide-melting temperatures, including a nearest-neighbor thermodynamic model for melting temperature.Abstract:
We developed OligoCalc as a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and doublestranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intramolecular hairpin loop formation. OligoCalc has a familiar ‘calculator’ look and feel, making it readily understandable and usable. OligoCalc incorporates three common methods for calculating oligonucleotide-melting temperatures, including a nearest-neighbor thermodynamic model for melting temperature. Since it first came online in 1997, there have been more than 900 000 accesses of OligoCalc from nearly 200 000 distinct hosts, excluding search engines. OligoCalc is available at http://basic.north western.edu/biotools/OligoCalc.html, with links to the full source code, usage patterns and statistics at that link as well.read more
Citations
More filters
Journal ArticleDOI
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
Anna Klindworth,Elmar Pruesse,Timmy Schweer,Jörg Peplies,Christian Quast,Matthias Horn,Frank Oliver Glöckner +6 more
TL;DR: The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies.
Journal ArticleDOI
Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton
TL;DR: It is demonstrated that a minor adjustment to the 806R primer will greatly increase detec- tion of the globally abundant SAR11 clade in marine and lake environments, and enable inclusion of this important bacterial lineage in experimental and environmental-based studies.
Journal ArticleDOI
MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species.
Masaki Miya,Yukuto Sato,Tsukasa Fukunaga,Tetsuya Sado,J. Y. Poulsen,Keiichi Sato,Toshifumi Minamoto,Satoshi Yamamoto,Hiroki Yamanaka,Hitoshi Araki,Michio Kondoh,Wataru Iwasaki +11 more
TL;DR: The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods and has the potential to serve as an alternative tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.
Journal ArticleDOI
Touchdown PCR for increased specificity and sensitivity in PCR amplification.
Darren Korbie,John S. Mattick +1 more
TL;DR: Touchdown (TD) PCR offers a simple and rapid means to optimize PCRs, increasing specificity, sensitivity and yield, without the need for lengthy optimizations and/or the redesigning of primers.
Journal ArticleDOI
Predominant archaea in marine sediments degrade detrital proteins
Karen G. Lloyd,Lars Schreiber,Dorthe Groth Petersen,Kasper Urup Kjeldsen,Mark A. Lever,Andrew D. Steen,Ramunas Stepanauskas,Michael Richter,Sara Kleindienst,Sabine Lenk,Andreas Schramm,Bo Barker Jørgensen +11 more
TL;DR: It is shown that the uncultured miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in the marine sub-sea floor and may have a previously undiscovered role in protein remineralization in anoxic marine sediments.
References
More filters
Book
Molecular Cloning: A Laboratory Manual
TL;DR: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years as mentioned in this paper and has been so popular, or so influential, that no other manual has been more widely used and influential.
Book
Molecular cloning : a laboratory manual
Joseph Sambrook,David W. Russell +1 more
TL;DR: The content has been entirely recast to include nucleic-acid based methods selected as the most widely used and valuable in molecular and cellular biology laboratories.
Journal ArticleDOI
Mfold web server for nucleic acid folding and hybridization prediction
TL;DR: The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large by making use of universally available web GUIs (Graphical User Interfaces).
Journal ArticleDOI
Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature.
J. Marmur,Paul Doty +1 more
TL;DR: The previously discovered linear relation between the base composition of DNA, expressed in percentage of guanine plus cytosine bases, and the denaturation temperature, T m, has been further investigated and it appears that the measurement of the T m is a satisfactory means of determining base composition in DNA.
Journal ArticleDOI
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
TL;DR: An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization and experimental constraints, derived from enzymatic and flavin mononucleotide cleavage, improve the accuracy of structure predictions.