Affiliation: Rensselaer Polytechnic Institute
- RNAML: a standard syntax for exchanging RNA informationAllison Waugh
Stanford Medical Informatics, Stanford University Medical Center, California 94305, USA
RNA 8:707-17. 2002..In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation...
- UNAFold: software for nucleic acid folding and hybridizationNicholas R Markham
Xerox Litigation Services, Albany, NY, USA
Methods Mol Biol 453:3-31. 2008..Users are encouraged to create their own scripts to supplement what comes with the package. This evolving software is available for download at http://www.bioinfo.rpi.edu/applications/hybrid/download.php ...
- DINAMelt web server for nucleic acid melting predictionNicholas R Markham
Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180 3590, USA
Nucleic Acids Res 33:W577-81. 2005..This server is connected to an active research program and should evolve as new theory and software are developed. The server URL is http://www.bioinfo.rpi.edu/applications/hybrid/...
- Mfold web server for nucleic acid folding and hybridization predictionMichael Zuker
Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
Nucleic Acids Res 31:3406-15. 2003..The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'...
- Prediction of hybridization and melting for double-stranded nucleic acidsRoumen A Dimitrov
Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
Biophys J 87:215-26. 2004....
- OligoArray: genome-scale oligonucleotide design for microarraysJean Marie Rouillard
Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 2136, USA
Bioinformatics 18:486-7. 2002..OligoArray is a program that computes gene specific and secondary structure free oligonucleotides for genome-scale oligonucleotide microarray construction or other applications...
- OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approachJean Marie Rouillard
Department of Chemical Engineering, University of Michigan, H H Dow, Ann Arbor, MI 48109, USA
Nucleic Acids Res 31:3057-62. 2003..OligoArray 2.0 was used to design 75 764 oligonucleotides representing 26 140 transcripts from Arabidopsis thaliana. Among this set, we provide at least one specific oligonucleotide for 93% of these transcripts...
- Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structureDavid H Mathews
Center for Human Genetics and Molecular Pediatric Disease, The Aab Institute of Biomedical Sciences, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 703, Rochester, NY 14642, USA
Proc Natl Acad Sci U S A 101:7287-92. 2004..For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs...
- RNA secondary structure predictionDavid H Mathews
University of Rochester, Rochester, New York, USA
Curr Protoc Nucleic Acid Chem . 2007..The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented...
- ALGORITHMS, THERMODYNAMICS AND STATISTICS FOR RNA FOLDINMichael Zuker; Fiscal Year: 2003..Partition function computations will be extended to allow folding constraints and to compute probabilities of foldings similar to a given one. ..