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altORFev / altORF evaluator
Predicts alternative open reading frames within eukaryotic mRNA translated by a conventional linear scanning mechanism and its modifications (leaky scanning, reinitiation). altORFev reveals efficiently translated alternative open reading frames (altORFs) recognized by the majority of 40S ribosomal subunits landing on the 5’-end of mRNA. It may be used to get additional information on eukaryotic genes taking into consideration alternative coding abilities of their mRNAs. altORFev uses an advanced linear scanning model with leaky scanning and reinitiation modules and thereby extends predictions provided by other tools which are commonly based on ribo-seq data analysis, evolutionary conservation of ORFs, or the basic linear scanning algorithm.
riboSeqR
Allows users to analyses sequencing data from ribosome profiling experiments. riboSeqR provides a set of methods for parsing ribosomal profiling data from multiple samples, aligning to coding sequences, inferring alternative reading frames, and plotting average and transcript-specific behavior of these data. It was developed to enable non-specialists to parse aligned Ribo-seq data, to identify the predominant lengths of ribosomal fragments and the codon positions to which they map, and to thus identify coding sequences undergoing translation.
RiboGalaxy
A freely available Galaxy-based web server for processing and analysing ribosome profiling data with the visualization functionality provided by GWIPS-viz. RiboGalaxy offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data. Researchers can take advantage of the published workflows which reduce the multi-step alignment process to a minimum of inputs from the user. Users can then explore their own aligned data as custom tracks in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks from published studies. In addition, users can assess the quality of their ribo-seq data, determine the strength of the triplet periodicity signal, generate meta-gene ribosome profiles as well as analyse the relative impact of mRNA sequence features on local read density.
systemPipeR
An extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of next-generation sequencing (NGS) applications. Its unique features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software on local computers and computer clusters. A flexible sample annotation infrastructure efficiently handles complex sample sets and experimental designs. To simplify the analysis of widely used NGS applications, systemPipeR provides pre-configured workflows and reporting templates for RNA-seq, ChIP-seq, VAR-seq and Ribo-seq.
riboviz
Allows convenient exploration and analysis of riboseq datasets. riboviz consists of a comprehensive and flexible backend analysis pipeline that allows the user to analyze their private unpublished dataset, along with a web application for comparison with previously published public datasets. It will increase the accessibility of new technology, increase research reproducibility, and offer a broadly useful toolkit for both the community of systems biologists who study genome-wide ribosome profiling data and also to research groups focused on individual genes of interest.
Shoelaces
New
Provides a tool for ribosome profiling data processing in small or large-scale studies. Shoelaces is based on a property of phasing and a 3-nucleotide periodicity of the reads stemming from coding regions to refine genuine translating footprints and calibrate P-site offsets. This software automatically chooses lengths and offsets, and allows batch-mode for processing multiple libraries in bulk. It offers either a command line and graphical interface: the command line can be included into an automated processing pipelines.
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