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rna parsingRNA secondary structure parsing, pseudoknots and other context-sensitive structures.
http://www.rnaparse.com/
RNA secondary structure parsing, pseudoknots and other context-sensitive structures.
http://www.rnaparse.com/
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James Lynn
PO b●●●●2382
Sol●●●tna , Alaska, 99669
United States
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James Lynn
PO b●●●●2382
Sol●●●tna , Alaska, 99669
United States
View this contact
James Lynn
PO b●●●●2382
Sol●●●tna , Alaska, 99669
United States
View this contact
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rna parsing | rnaparse.com Reviews
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RNA secondary structure parsing, pseudoknots and other context-sensitive structures.
rnaparse.com
Pseudoknots
http://www.rnaparse.com/Pseudoknots.html
The methods we use here essentially ignore rna molecular energy and “look” or match a specific configuration which can then be further verified via slower and more computationally expensive methods. This grammatical method bypasses the NP problem of trying every possible fitting permutation by instead matching a predefined system of stems and loops in a linear fashion. Http:/ rnavlab.utep.edu/portal rna searchable database. Http:/ www.ekevanbatenburg.nl/PKBASE/PKB.HTML Pseudobase. A context-sensitive gra...
Introduction
http://www.rnaparse.com/Introduction.html
Secondary Structure vs. Linear Nucleotide Composition. Consider the following functional, NC RNA where:. N= Any nucleotide {a,u,g,c}. C= W/C or wobble pair compliment {a-u, u-a, g-c, c-g, g-u, u-g}. Testing all possible nucleotide sequences that could possibly form the molecule above is impossible, matching structure via grammatical predicates is quite easy. RNA is treated as if it where a language:Languages can be classified by order of complexity and of interdependency. RNA structure is matched via gra...
about
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All Possible Patterns for an RNA String with Example Grammars. James F. Lynn RNAparse/www.RNAparse.com 2012. The reader should be familiar with basic RNA secondary structure determination and rudimentary formal grammar theory. Some elementary formal grammars in BNF-like style are used to show how a string with self-referential properties can be. Described with an AFFIX operator that in essence attaches one part of the string to another. In the text, least-energy. And context sensitive grammars. C' rho(x ...
Selected Publications
http://www.rnaparse.com/Selected_Publications.html
Covariant/Substitution Structures of a Ribosomal-Like Pseudoknot. Complexity and RNA Science - artical. Tandem Complement Repeats - A New Standard Notation.
Tools Links
http://www.rnaparse.com/Tools__Links.html
Rna Parse Tools and Links. Online Tools and Links Used in Bio-Genetic research. Outstanding freeware for drawing RNA structures often used by this site. National Center for Biotechnology Information. A general purpose multiple sequence alignment program for DNA or proteins. Families database of alignments and CMs. Human mitochondrial genome database. Viral RNA Structure Database. Human (Homo sapiens) Genome Browser Gateway. Vienna RNA Sequence Design. Vienna RNA Secondary Structure.
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Current events | Rnaparse's Blog
https://rnaparse.wordpress.com/2011/10/15/current-events
Data Base Tandem Compliment Repeats. October 15, 2011. We are juggling with several software applications in bioinformatics as well as some other more-commercial apps not specifically associated with science research or mentioned in http:/ www.rnaparse.com. From → Uncategorized. Leave a Reply Cancel reply. Enter your comment here. Fill in your details below or click an icon to log in:. Address never made public). You are commenting using your WordPress.com account. ( Log Out. Some Theory on RNA Strings.
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rna parsing
Complex RNA Secondary Structure Prediction:. RNA Motif Classification Grammars Including Pseudoknots and Tandem Compliment Repeats. Of the secondary structures it may form. If you are seeking specific structures, pseudoknots and tandem compliment repeats included, we can assist in your research with custom parsing of raw genetic sequences. Soldotna, Alaska 99669. RNA parse is in part supported through independent, corporate and academic gifts and grants. Thank you for supporting this research.
Rnaparse's Blog | www.rnaparse.com
Data Base Tandem Compliment Repeats. February 11, 2014. I have completed a program that uses system of grammars that learn from input, and using what they learn to parse a set of unknown words to see if they check against the original set. There are 3 files needed:. Learn set: containing words, letters, numbers, names etc. Rule Set: empty until filled with automatically written rules. Test Set: containing words, letters, numbers, names etc. Eg the learn file contains the word “hello”. January 2, 2014.
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