# HG changeset patch # User rnateam # Date 1489442575 14400 # Node ID 51261dff08a574d3050468385434b2eb375ccb73 # Parent 606440a3852d2bf3715144923bf88c730588766c planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit f971832d2b34a182314e5201ea6895dd207c5923 diff -r 606440a3852d -r 51261dff08a5 locarna_best_subtree.xml --- a/locarna_best_subtree.xml Mon Feb 27 12:02:38 2017 -0500 +++ b/locarna_best_subtree.xml Mon Mar 13 18:02:55 2017 -0400 @@ -1,6 +1,6 @@ - graphclust-wrappers + graphclust-wrappers locarna rnaz perl-math-round @@ -11,9 +11,16 @@ - - - - + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -125,127 +129,8 @@ organization={Omnipress} } - @Article{Will_Joshi_Hofacker-LocAR_Accur_bound-2012, - author = {Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and - Stadler, Peter F. and Backofen, Rolf}, - title = {{LocARNA}-{P}: {Accurate} boundary prediction and improved - detection of structural {RNAs}}, - journal = {RNA}, - year = {2012}, - volume = {18}, - number = {5}, - pages = {900-14}, - user = {will}, - pmid = {22450757}, - doi = {10.1261/rna.029041.111}, - issn = {1469-9001}, - issn = {1355-8382}, - abstract = {Current genomic screens for noncoding RNAs (ncRNAs) predict - a large number of genomic regions containing potential - structural ncRNAs. The analysis of these data requires - highly accurate prediction of ncRNA boundaries and - discrimination of promising candidate ncRNAs from weak - predictions. Existing methods struggle with these goals - because they rely on sequence-based multiple sequence - alignments, which regularly misalign RNA structure and - therefore do not support identification of structural - similarities. To overcome this limitation, we compute - columnwise and global reliabilities of alignments based on - sequence and structure similarity; we refer to these - structure-based alignment reliabilities as STARs. The - columnwise STARs of alignments, or STAR profiles, provide a - versatile tool for the manual and automatic analysis of - ncRNAs. In particular, we improve the boundary prediction of - the widely used ncRNA gene finder RNAz by a factor of 3 from - a median deviation of 47 to 13 nt. Post-processing RNAz - predictions, LocARNA-P's STAR score allows much stronger - discrimination between true- and false-positive predictions - than RNAz's own evaluation. The improved accuracy, in this - scenario increased from AUC 0.71 to AUC 0.87, significantly - reduces the cost of successive analysis steps. The - ready-to-use software tool LocARNA-P produces - structure-based multiple RNA alignments with associated - columnwise STARs and predicts ncRNA boundaries. We provide - additional results, a web server for LocARNA/LocARNA-P, and - the software package, including documentation and a pipeline - for refining screens for structural ncRNA, at - http://www.bioinf.uni-freiburg.de/Supplements/LocARNA-P/.} -} - - @Article{Will:etal:_infer_non_codin_rna_famil:PLOS2007, - author = {Sebastian Will and Kristin Reiche and Ivo L. Hofacker and - Peter F. Stadler and Rolf Backofen}, - title = {Inferring Non-Coding {RNA} Families and Classes by Means of - Genome-Scale Structure-Based Clustering}, - journal = {PLoS Comput Biol}, - year = 2007, - volume = {3}, - number = {4}, - pages = {e65}, - issn = {1553-7358}, - issn = {1553-734X}, - pmid = {17432929}, - doi = {10.1371/journal.pcbi.0030065}, - user = {will}, - abstract = {The RFAM database defines families of ncRNAs by means of - sequence similarities that are sufficientto establish - homology. In some cases, such as microRNAs, box H/ACA - snoRNAs, functional commonalities define classes of RNAs - that are characterized by structural similarities, and - typically consist ofmultiple RNA families. Recent advances - in high-throughput transcriptomics and comparative genomics - have produced very large sets of putative non-coding RNAs - and regulatory RNA signals. For many ofthem, evidence for - stabilizing selection acting on their secondary structures - has been derived, and at least approximate models of their - structures have been computed. The overwhelming majority of - these hypo-thetical RNAs cannot be assigned to established - families or classes. We present here a structure-based - clustering approach that is capable of extracting putative - RNA classesfrom genome-wide surveys for structured RNAs. The - LocARNA tool implements a novel variant of theSankoff - algorithm that is sufficiently fast to deal with several - thousand candidate sequences. The method is also robust - against false positive predictions, i.e., a contamination of - the input data with unstructured ornon-conserved - sequences. We have successfully tested the LocARNA-based - clustering approach on the sequences of the - RFAM-seedalignments. Furthermore, we have applied it to a - previously published set of 3332 predicted structured - elements in the Ciona intestinalis genomes (Missal et al., - Bioinformatics 21(S2), i77-i78). In addition torecovering - e.g. tRNAs as a structure-based class, the method identifies - several RNA families, including microRNA and snoRNA - candidates, and suggests several novel classes of ncRNAs for - which to-date norepresentative has been experimentally - characterized.} -} - - - @Article{Smith:Heyne:Richter:Freib_RNA_Tools:NAR2010, - author = {Smith, Cameron and Heyne, Steffen and Richter, Andreas S. - and Will, Sebastian and Backofen, Rolf}, - title = {Freiburg {RNA} {Tools}: a web server integrating {IntaRNA}, - {ExpaRNA} and {LocARNA}}, - journal = NAR, - year = {2010}, - volume = {38 Suppl}, - number = {}, - pages = {W373-7}, - user = {arichter}, - pmid = {20444875}, - doi = {10.1093/nar/gkq316}, - issn = {0305-1048}, - issn = {1362-4962}, - abstract = {The Freiburg RNA tools web server integrates three tools - for the advanced analysis of RNA in a common web-based user - interface. The tools IntaRNA, ExpaRNA and LocARNA support - the prediction of RNA-RNA interaction, exact RNA matching - and alignment of RNA, respectively. The Freiburg RNA tools - web server and the software packages of the stand-alone - tools are freely accessible at - http://rna.informatik.uni-freiburg.de.} -} - + 10.1261/rna.029041.111 + 10.1371/journal.pcbi.0030065 + 10.1093/nar/gkq316