RNAhybridR: Find minimum free energy hybridisations of a long (target)...
In Santaris/seqtools: Tools for oligonucleotide-centric sequence analysis
Description
Usage
Arguments
Examples
Description
This function is the R version of RNAhybrid by Rehmsmeier et al., RNA, 10:1507-1517, 2004.
The hybridisation is performed in a kind of domain mode, ie. the short sequence is hybridised
to the best fitting parts of the long one. The command line tool RNAhybrid
needs to be installed (version 2.1 from http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/dl_pre-page.html).
There is no I/O activity so this function can be easily parallelized.
Usage
1
RNAhybridR(seq.target, seq.query, b = 1)
Arguments
seq.target
a character vector with the long nucleotide sequence
seq.query
a character vector with the short nucleotide sequence
b
maximal number of hits to show. Hits with increasing minimum free energy
(reminder: larger energies are worse) are shown untill there are no more hits.
Hits may only overlap at dangling bases (5' or 3' unpaired end of target).
Examples
1
a <- RNAhybridR("AACCTTGG", "ACTG")
Santaris/seqtools documentation built on May 9, 2019, 12:44 p.m.
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Description Usage Arguments Examples
Description
This function is the R version of RNAhybrid by Rehmsmeier et al., RNA, 10:1507-1517, 2004. The hybridisation is performed in a kind of domain mode, ie. the short sequence is hybridised to the best fitting parts of the long one. The command line tool RNAhybrid needs to be installed (version 2.1 from http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/dl_pre-page.html). There is no I/O activity so this function can be easily parallelized.
Usage
1 | RNAhybridR(seq.target, seq.query, b = 1)
|
Arguments
seq.target |
a character vector with the long nucleotide sequence |
seq.query |
a character vector with the short nucleotide sequence |
b |
maximal number of hits to show. Hits with increasing minimum free energy (reminder: larger energies are worse) are shown untill there are no more hits. Hits may only overlap at dangling bases (5' or 3' unpaired end of target). |
Examples
1 | a <- RNAhybridR("AACCTTGG", "ACTG")
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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