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Protocols

RNAProfile specifications

Information


Unique identifier OMICS_08114
Name RNAProfile
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publications for RNAProfile

RNAProfile citations

 (3)
library_books

RNA motif discovery: a computational overview

2015
Biol Direct
PMCID: 4600295
PMID: 26453353
DOI: 10.1186/s13062-015-0090-5

[…] ee occurs as a sub-graph of the data tree in the sense that if node b is a child of node a in the pattern tree, then the node in the data tree associated with node b need to only be a descendant of a.RNAProfile [] is a relatively simple method with a heuristic approach. The approach in principle is very similar to the initialization step of CMfinder to build the initial alignments. It also takes a […]

call_split

Classification and assessment tools for structural motif discovery algorithms

2013
BMC Bioinformatics
PMCID: 3698030
PMID: 23902564
DOI: 10.1186/1471-2105-14-S9-S4
call_split See protocol

[…] cover structural motifs in more than two input sequences, where the input sequences are different, but share a common RNA structure. Among the surveyed tools, we were able to obtain six: CMfinder [], RNAProfile [], RNAmine [], comRNA [], RNAPromo [], and Seed []. Our first observation is that the use of structural discovery tools often requires knowledge of the Unix operating system. Except for RN […]

library_books

A computational method to predict genetically encoded rare amino acids in proteins

2005
Genome Biol
PMCID: 1242214
PMID: 16168086
DOI: 10.1186/gb-2005-6-9-r79

[…] ted ORFs passing the previous tests in each bacterial organism. The extracted set of RNA sequences for each organism was used to detect a common, single hairpin motif using the rapid, heuristic-based RNAPROFILE program []. A test calculation predicted the known SECIS element of the gene encoding FDH from E. coli correctly [] (Figure ). The putative SECIS hairpin motifs were manually inspected for […]

Citations

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RNAProfile institution(s)
Dipartimento di Bioscienze, Università di Milano, Milano, Italy

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