Curator Dashboard

A software tool for plant miRNA and target identification. C-mii pipelines are based on combined steps and criteria from previous studies and also incorporated with several tools such as standalone BLAST and UNAFold and pre-installed databases including miRBase, UniProt, and Rfam. C-mii provides following distinguished features. First, it comes with graphical user interfaces of well-defined pipelines for both miRNA and target identifications with reliable results. Second, it provides a set of filters allowing users to reduce the number of results corresponding to the recently proposed constraints in plant miRNA and target biogenesis. Third, it extends the standard computational steps of miRNA target identification with miRNA-target folding module and GO annotation. Fourth, it supplies the bird eye views of the identification results with info-graphics and grouping information. Fifth, it provides helper functions for database update and auto-recovery to ease system usage and maintenance. Finally, it supports the multi-project and multi-thread management to improve the computational speed.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A Bayesian decision fusion algorithm for microRNA target prediction that combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and DianamicroT. Users enter a Ref_seq ID for a query target gene and select a miRNA, which BCmicrO will use in its predictive algorithm. The prediction results can then be downloaded.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Software / Web Server to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Institute for genetics, through National BioResource Project, collects, preserves, and provides bio-resources (strains, populations, tissues, cells, genes of animals, plants and microorganisms, and information on these materials for R&D use) that are essential for life science research.

• Organization
• SciCrunch
• 17 years ago - submitted by Eddy Kim

Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file).

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A software tool developed to process and analyze small RNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes. ShortStack discovers small RNA ''clusters'' de novo, based on user-set thresholds, and annotates clusters with respect to small RNA size, orientation, and repetitiveness. ShortStack also discovers and annotates MIRNA genes, and other Hairpin-associated small RNA genes. In addition, ShortStack includes a robust method to detect genes producing small RNAs in a phased manner. It outputs a descriptive table of all results, useful genome browser tracks, a table describing the results of the hairpin / MIRNA analysis for each cluster, and detailed text-based alignments of all MIRNAs and hairpin-associated clusters. It can also be run in ''count'' mode, to quantify a set of input loci with genomic coordinates determined a priori by the user. ShortStack is a perl program. Besides perl, ShortStack also requires samtools and the RNALfold and RNAeval programs from the Vienna RNA Package to execute. When used to control the alignment of small RNA data to a reference genome, ShortStack also requires bowtie and bowtie-build. Finally, for optimal results, ShortStack uses a file of inverted repeats produced by the EMBOSS application einverted.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Pipeline scripts for creating a miRspring (miRNA sequence profiling) document, a new way of sharing and analysing sequencing data for small RNA.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A stand-alone software package implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A web tool for simple microRNA prediction in genome sequences.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A machine learning software package that can predict the precursor class of small RNAs present in a high-throughput RNA-sequencing dataset. In addition to classification, it also produces information about the features that are most important for discriminating different populations of small non-coding RNAs.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Japanese national research university located in Chikusa-ku, Nagoya. It was the seventh Imperial University in Japan, one of the first five Designated National University and selected as a Top Type university of Top Global University Project by the Japanese government.

• Organization
• SciCrunch
• 17 years ago - submitted by Stephen Larson

An algorithm to identify chromosomal breakpoints using massively parallel next generation sequence data.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Designed to identify CNVs between two genomes.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Copy number estimation from read depth information.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Prediction of copy number alterations and loss of heterozygosity using deep-sequencing data.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation.

• Resource
• SciCrunch
• 13 years ago - by Anonymous