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Translated open reading frame detection software tools | Ribosome profiling data analysis

Ribosome profiling via high-throughput sequencing (ribo-seq) is a promising new technique for characterizing the occupancy of ribosomes on messenger RNA (mRNA) at base-pair resolution. The ribosome is responsible for translating mRNA into proteins,…
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RiboTaper
Desktop

RiboTaper

A rigorous statistical approach that identifies translated regions on the basis…

A rigorous statistical approach that identifies translated regions on the basis of the characteristic three-nucleotide periodicity of Ribo-seq data. We used RiboTaper with deep Ribo-seq data from…

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ORF-RATER
Desktop
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ORFscore
Desktop

ORFscore

Allows users to detect actively translated small open reading frames (smORFs).…

Allows users to detect actively translated small open reading frames (smORFs). ORFscore quantifies the biased distribution of ribosome-protected fragments (RPFs) toward the first frame of a given…

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FLOSS
Desktop

FLOSS Fragment Length Organization Similarity Score

Measures the magnitude of disagreement between these two distributions taking…

Measures the magnitude of disagreement between these two distributions taking into account lower scores reflecting higher similarity. FLOSS is able to identify effect of the small number of lncRNAs…

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riboHMM
Desktop

riboHMM

Allows users to identify translated coding sequences (CDSs) by leveraging both…

Allows users to identify translated coding sequences (CDSs) by leveraging both the total abundance and the codon periodicity structure in ribosome-protected RNA fragments (RPFs). riboHMM utilizes…

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RibORF
Desktop

RibORF

Allows users to analyze ribosomal profiling data and identify translated open…

Allows users to analyze ribosomal profiling data and identify translated open reading frames (ORFs). RibORF is useful for the detection of ORFs that combines alignment of ribosomal A-sites, 3-nt…

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Rp-Bp
Desktop

Rp-Bp Ribosome profiling with Bayesian predictions

Represents an unsupervised Bayesian approach. Rp-Bp allows users to identify…

Represents an unsupervised Bayesian approach. Rp-Bp allows users to identify translated open reading frames (ORFs) based on ribosome profiles. It detects all translated ORFs which exhibit this…

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RiboProfiling
Desktop

RiboProfiling

Offers a collection of tools for Ribo-seq data analysis. RiboProfiling provides…

Offers a collection of tools for Ribo-seq data analysis. RiboProfiling provides a unique, straightforward R implementation of a ribosome profiling pipeline from BAM, to P-site calibration,…

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REPARATION
Desktop

REPARATION RibosomeE Profiling Assisted (re-)AnnotaTION

Deduces intrinsic characteristics from data and thus can be applied to Ribo-seq…

Deduces intrinsic characteristics from data and thus can be applied to Ribo-seq data targeting elongating ribosomes. REPARATION is an application that trains an ensemble classifier to learn Ribo-seq…

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RiboCode
Desktop

RiboCode

Allows the assessment of non-canonical translations such as overlapping open…

Allows the assessment of non-canonical translations such as overlapping open reading frames (ORFs). RiboCode is a statistically method for the de novo annotation of the full translatome by…

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SPECtre
Desktop

SPECtre

A spectral coherence-based classification algorithm to identify regions of…

A spectral coherence-based classification algorithm to identify regions of active translation using aligned ribosome profiling sequence reads. SPECtre leverages a key feature of ribosome profiling…

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