:: DESCRIPTION
ShortFuse is a software to identify fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Apr 15;27(8):1068-75. Epub 2011 Feb 16.
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V.
:: DESCRIPTION
RSEQtools is a suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments. MRF was developed to address privacy concerns associated with the potential for mRNA sequence reads to identify and genetically characterise specific individuals; it is a compact data summary format that enables anonymization of confidential sequence information, while maintaining the ability to conduct subsequent functional genomics studies. RSEQtools provides a suite of modules that convert to/from MRF data and perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Lukas Habegger*, Andrea Sboner*, Tara A. Gianoulis, Joel Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein.
RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
Bioinformatics (2011) 27 (2): 281-283.
:: DESCRIPTION
IQSeq is a tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Jiang Du, Jing Leng, Lukas Habegger, Andrea Sboner, Drew McDermott, Mark Gerstein.
“IQSeq: Integrated Isoform Quantification Analysis Based on Next-generation Sequencing”
PLoS ONE 7(1): e29175. doi:10.1371/journal.pone.0029175
:: DESCRIPTION
RNApathfinder is a web server to compute near-optimal folding pathways between two given secondary structures for a given RNA sequence. Since this problem is known to be NP-complete, our main algorithm, RNAtabupath uses the TABU local search heuristic. The web server includes both downloadable source code for several algorithms, as well as a web engine to compute pathways. Intended applications concern folding pathways for RNA conformational switches.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
I. Dotú, W.A. Lorenz, P. Van Hentenryck, P. Clote.
Computing folding pathways between RNA secondary structures.
Nucleic Acids Res. 2010 Mar 1;38(5):1711-22.
:: DESCRIPTION
RNAborMEA computes the maximum expected accurate δ-neighbors of a given RNA secondary structure for a given RNA sequence. Here, a structure T is a δ-neighbor of a given structure S, if S can be transformed into T by a minimum number δ of edit operations, where an edit operation consists of removing or adding a single base pair (i.e. if the base pair distance between S and T is δ).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Feng Lou and Peter Clote.
Maximum expected accurate structural neighbors of an RNA secondary structure.
Proceedings of 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), Feb 3-5, 2011. Orlando, FL.
:: DESCRIPTION
RD is intended to implement a program for statistical estimation of isoform expression levels using RNA-Seq based on the modeling of RNA degradation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wan L, Yan XT, Chen T and Sun FZ (2011)
RD: A Program for Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
submitted.
:: DESCRIPTION
RNACluster is an integrated computational software which implements 6 common structure distances to measure the (dis)similarity of RNA secondary structures including base pair distance, mountain distance, morphological distance, tree edit distance, string edit distance and our in-house structure matrix distance, and one effective cluster approach for the ensemble clustering using a minimum spanning tree (MST) based algorithm. RNACluster can be used to study the characteristics of RNA secondary structures, RNA structure conformational switches, RNA conformational energy landscapes and RNA secondary structure prediction based on the clustering of structure ensemble.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Liu Q, Olman V, Liu H, Ye X, Qiu S, Xu Y.
RNACluster: An integrated tool for RNA secondary structure comparison and clustering.
J Comput Chem. 2008 Jul 15;29(9):1517-26.
:: DESCRIPTION
BBSeq (Beta-Binomial modeling of the overdispersion of the RNA-seq count data)is used to identify differential expression in high-throughput count data, such as RNAseq count data which is derived from next-generation sequencing machines. Our modeling design is very flexible. It can not only solve the data with multiple comparisons, but also can find the affect from other covariates, such as age and other counfounding variables.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhou YH, Xia K, Wright FA. (2011)
A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data.
Bioinformatics (2011) 27 (19): 2672-2678.
:: DESCRIPTION
The FDM (Flow Difference Metric) identifies regions of differential RNA-transcript expression between pairs of splice graphs, without need for an underlying gene model or catalog of transcripts. We present a novel non-parametric statistical test between splice graphs to assess the significance of differential transcription, and extend it to group-wise comparison incorporating sample replicates.
::DEVELOPER
Bioinformatics Lab @CS.UKy.edu
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Darshan Singh, et al
FDM: A Graph-based Statistical Method to Detect Differential Transcription using RNA-seq data
Bioinformatics (2011) doi: 10.1093
:: DESCRIPTION
SimTree is an online tool for computing the similarity between RNA secondary structures.
::DEVELOPER
Eran Eden , Izhar Wallach (izharw@keddem.com) ,Zohar Yakhini @ Laboratory of Computational Biology , Technion
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
