:: DESCRIPTION
PALMA aligns two genomic sequences in an optimal way according to its underlying algorithm and trained parameters.
::DEVELOPER
the Biomedical Informatics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2007 Aug 1;23(15):1892-900. Epub 2007 May 30.
PALMA: mRNA to genome alignments using large margin algorithms.
Schulze U, Hepp B, Ong CS, Rätsch G.
:: DESCRIPTION
rNA (randomized Numerical Aligner) is a software able to align the huge amount of data produced by Next Generation Sequencers. The main feature of rNA is the fact that it achieves an accuracy greater than the majority of other tools in a feasible amount of time. rNA works with single as well as paired ends reads and it allows indels and delta-search for better accuracy.
mrNA is the MPI version of the original rNA program.
grNA is a graphical front-end for rNA
::DEVELOPER
bioinformatics team at Istituto di Genomica Applicata (Applied Genomics Institute) andDepartment of Mathematics and Informatics, University of Udine.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
rNA: a Fast and Accurate Short Reads Numerical Aligner
Vezzi F., Del Fabbro C., Tomescu A.I., and Policriti A.
Bioinformatics, 2011, doi:10.1093/bioinformatics/btr617
mrNA: the MPI randomized Numerical Aligner
Del Fabbro C., Vezzi F., and Policriti A.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta (Georgia), November 12-15, 2011, IEEE Computer Society 0:139-142, ISBN 978-0-7695-4574-5
:: DESCRIPTION
PACES is a tool to predict N4-acetylcytidine (ac4C) modification sites on the mRNA sequences.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Zhao W, Zhou Y, Cui Q, Zhou Y.
PACES: prediction of N4-acetylcytidine (ac4C) modification sites in mRNA. Sci Rep.
2019 Jul 31;9(1):11112. doi: 10.1038/s41598-019-47594-7. PMID: 31366994; PMCID: PMC6668381.
:: DESCRIPTION
miRlastic is a novel method which infers miRNA-target interactions using transcriptomic data as well as prior knowledge and performs functional annotation of target genes by exploiting the local structure of the inferred network.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma.
Sass S, Pitea A, Unger K, Hess J, Mueller NS, Theis FJ.
Int J Mol Sci. 2015 Dec 18;16(12):30204-22. doi: 10.3390/ijms161226230.
:: DESCRIPTION
iSeeRNA is a support vector machine (SVM)-based classifier for the identification of lincRNAs.
::DEVELOPER
Dr. Sun Hao’s Bioinformatics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Genomics. 2013;14 Suppl 2:S7. doi: 10.1186/1471-2164-14-S2-S7. Epub 2013 Feb 15.
iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data.
Sun K1, Chen X, Jiang P, Song X, Wang H, Sun H.
:: DESCRIPTION
X2K (Expression2Kinases) is a method to identify upstream regulators likely responsible for observed patterns in genome-wide gene expression. By integrating ChIP-seq/chip and position-weight-matrices (PWMs) data, protein-protein interactions, and kinase-substrate phosphorylation reactions, X2K can better identify regulatory mechanisms upstream of genome-wide differences in gene expression. X2K first infers the most likely transcription factors that regulate the differences in gene expression, then use protein-protein interactions to connect the identified transcription factors using additional proteins for building transcriptional regulatory subnetworks centered on these factors, and finally use kinase-substrate protein phosphorylation reactions, to identify and rank candidate protein-kinases that most likely regulate the formation of the identified transcriptional complexes.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH, Ma’ayan A.
Expression2Kinases: mRNA Profiling Linked to Multiple Upstream Regulatory Layers.
Bioinformatics. (2012) 28 (1): 105-111
:: DESCRIPTION
mirConnX is a user-friendly web interface for inferring, displaying and parsing mRNA and microRNA (miRNA) gene regulatory networks. mirConnX combines sequence information, and computational predictions with gene expression data analysis to create a disease-specific, genome-wide regulatory network.
::DEVELOPER
SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W416-23. doi: 10.1093/nar/gkr276. Epub 2011 May 10.
mirConnX: condition-specific mRNA-microRNA network integrator.
Huang GT, Athanassiou C, Benos PV.
:: DESCRIPTION
mRIN (mRNA integrity number) is a computational method to assess a quantitative measure of mRNA integrityta. This is done by quantitatively modeling of the 3′ bias of read coverage profiles along each mRNA transcript. A per-sample summary mRIN is then derived as an indicator of mRNA degradation. This method has been used for systematic analysis of large scale RNA-Seq data of postmortem tissues, in which RNA degradation during tissue collection is particularly an issue.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Commun. 2015 Aug 3;6:7816. doi: 10.1038/ncomms8816.
mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data.
Feng H, Zhang X, Zhang C
:: DESCRIPTION
ASARP is a pipeline for accurate identification of allele-specific alternative mRNA processing
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2012 Jul;40(13):e104. doi: 10.1093/nar/gks280. Epub 2012 Mar 29.
Identification of allele-specific alternative mRNA processing via transcriptome sequencing.
Li G1, Bahn JH, Lee JH, Peng G, Chen Z, Nelson SF, Xiao X.
:: DESCRIPTION
SNPfold evaluates the effects of SNPs (Single Nucleotide Polymorphisms) on the ensemble structure of an RNA. It takes as input an RNA sequence and one or more SNPs, and then evaluates the structural consequences of the mutation by computing a WT/SNP correlation coefficient. The smaller the correlation the larger the structural effects of the SNP.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS Genet. 2010 Aug 19;6(8):e1001074. doi: 10.1371/journal.pgen.1001074.
Disease-associated mutations that alter the RNA structural ensemble.
Halvorsen M, Martin JS, Broadaway S, Laederach A.
