Ribosome profiling data analysis bioinformatics software tools

Genome-wide analyses of gene expression have so far focused on the abundance of mRNA species as measured either by microarray or, more recently, by RNA sequencing. However, neither approach provides information on protein synthesis, which is the true end point of gene…

Ribo-seq analysis steps

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RRS
Desktop

RRS Ribosome Release Score

Identifies functional protein-coding transcripts with greater sensitivity by…

Identifies functional protein-coding transcripts with greater sensitivity by detecting the termination of translation at the end of an open reading frame. RRS is well-suited to distinguish real…

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SMoPT
Desktop

SMoPT

Describes translation dynamics to the single-nucleotide resolution for entire…

Describes translation dynamics to the single-nucleotide resolution for entire transcriptome. SMoPT is based on a Markov model of translation using the Gillespie algorithm. It treats the total number…

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CSCPD
Desktop

CSCPD Cumulative SubCodon Proportion Difference

Exploits the subcodon ribosome protected fragment (RPF) periodicity signature…

Exploits the subcodon ribosome protected fragment (RPF) periodicity signature to identify mRNA transcripts with putative reading frame transitions. CSCPD allows dually coded regions to be detected…

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PTS
Desktop

PTS Periodicity Transition Score

Permits analysis of subcodon profiles. PTS is calculated as the sum of excess…

Permits analysis of subcodon profiles. PTS is calculated as the sum of excess areas for each subcodon position. It can be used as an indicator of a frame transition in an mRNA. This software performs…

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TASEP
Algorithm

TASEP Totally ASymmetric Exclusion Process

Models translation using statistical and computational methods. TASEP is based…

Models translation using statistical and computational methods. TASEP is based on an efficient initiation rate approximation scheme combined with a novel Monte Carlo simulation strategy inside an…

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Plastid
Desktop

Plastid

Allows users to analyze nucleotide-resolution of genomics data. Plastid can…

Allows users to analyze nucleotide-resolution of genomics data. Plastid can extract the relevant biological information from various properties of raw read alignments. It provides consistent…

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RiboAsiteDeblur
Desktop

RiboAsiteDeblur

Recovers the A-site positions from ribosome profiling data. RiboAsiteDeblur…

Recovers the A-site positions from ribosome profiling data. RiboAsiteDeblur enables comparisons of ribosome profiling data from different replicates, conditions, and laboratories. It does not assume…

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RiboPip
Desktop

RiboPip

Enables users to process Ribosome Profiling (Ribo-seq) and RNA sequencing…

Enables users to process Ribosome Profiling (Ribo-seq) and RNA sequencing (RNA-seq) datasets. RiboPip computes a splice-aware alignment to a reference database along with a read summarization and…

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