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Coding and noncoding region discrimination software tools | Gene expression data analysis

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis…
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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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COME
Desktop

COME COding potential calculation tool based on Multiple fEatures

Predicts the coding potential for a given transcript. COME integrates multiple…

Predicts the coding potential for a given transcript. COME integrates multiple sequence-derived and experiment-based features using a decompose-compose method, which makes COME’s performance more…

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PLncPRO
Desktop

PLncPRO Plant Long Non-Coding RNA Prediction by Random fOrest

Discovers long non-coding RNAs (lncRNAs) in plants via classifying coding and…

Discovers long non-coding RNAs (lncRNAs) in plants via classifying coding and long non-coding transcripts. PLncPRO allows prediction of lncRNAs in plants based on various sequence features extracted…

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longdist
Desktop

longdist

Reduces the number of features calculated from nucleotides of transcripts.…

Reduces the number of features calculated from nucleotides of transcripts. longdist is a Support Vector Machine (SVM) based method to distinguish long non-coding RNAs (lncRNAs) from protein coding…

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DiSCO-Bac
Dataset

DiSCO-Bac Discovery of sRNA Coding ORFs in Bacteria

Provides a broad survey of protein coding in bacterial small RNAs (sRNAs).…

Provides a broad survey of protein coding in bacterial small RNAs (sRNAs). DiSCO-Bac combines summary results, individual open reading frame (ORF) characteristics, and tools for sorting and…

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lncScore
Desktop

lncScore

Identifies the long non-coding RNAs (lncRNAs) from the assembled novel…

Identifies the long non-coding RNAs (lncRNAs) from the assembled novel transcripts. lncScore can also be used to calculate the coding potential. This alignment-free tool uses a logistic regression…

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mRNN
Desktop

mRNN mRNA Recurrent Neural Network

Predicts protein-coding potential on transcripts. mRNN is capable of learning…

Predicts protein-coding potential on transcripts. mRNN is capable of learning true defining features of mRNAs, including trinucleotide patterns and depletion of in-frame stop codons after the start…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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LncRNA-ID
Desktop

LncRNA-ID

Calculates the coding potential of a transcript using a machine learning model…

Calculates the coding potential of a transcript using a machine learning model (random forest) based on multiple features including sequence characteristics of putative open reading frames,…

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PhyloCSF
Desktop

PhyloCSF

A method to determine whether a multi-species nucleotide sequence alignment is…

A method to determine whether a multi-species nucleotide sequence alignment is likely to represent a protein-coding region. It does not rely on homology to known protein sequences; instead, it…

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CNCI
Desktop

CNCI Coding-Non-Coding Index

A powerful signature tool by profiling adjoining nucleotide triplets to…

A powerful signature tool by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for…

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CPAT
Desktop
Web

CPAT Coding Potential Assessment Tool

An alignment-free method which rapidly recognizes coding and noncoding…

An alignment-free method which rapidly recognizes coding and noncoding transcripts from a large pool of candidates. The software accepts input sequences in either FASTA- or BED-formatted data files.

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GPGA
Algorithm

GPGA Gene Prediction with Genetic Algorithm

A gene prediction technique based on Genetic Algorithm (GA) for determining the…

A gene prediction technique based on Genetic Algorithm (GA) for determining the optimal positions of exons of a gene in a chromosome or genome. GPGA reduces the problem of correct identification of…

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FEELnc
Desktop

FEELnc FlExible Extraction of LncRNAs

An alignment-free program which accurately annotates lncRNAs based on a Random…

An alignment-free program which accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames. Benchmarking…

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ALPS
Desktop

ALPS alignment of pattern matrices score

Classifies ncRNAs by using primary information from a deep sequencing…

Classifies ncRNAs by using primary information from a deep sequencing experiment, i.e. the relative positions and lengths of reads. ALPS is not designed to recognize a certain class of ncRNA, it can…

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FrameDP
Web
Desktop

FrameDP

Predicts Coding Data Sequence in transcripts. FrameDP can adapt itself to…

Predicts Coding Data Sequence in transcripts. FrameDP can adapt itself to different levels of sequence qualities. It provides an automatic protein description based on InterPro domain content. The…

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PLEK
Desktop
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RNAcode
Desktop

RNAcode

A program to detect coding regions in multiple sequence alignments that is…

A program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. It is open source software and…

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QRNA
Desktop

QRNA

Provides a prototype noncoding RNA genefinder, based on comparative genome…

Provides a prototype noncoding RNA genefinder, based on comparative genome sequence analysis. QRNA detects conserved RNA secondary structures, including both ncRNA genes and cis-regulatory RNA…

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PORTRAIT
Desktop
Web

PORTRAIT

An algorithm for identifying non-coding RNAs on a transcriptome context. It can…

An algorithm for identifying non-coding RNAs on a transcriptome context. It can be integrated into pipelines, and provides a low computational cost solution for ncRNA detection in transcriptome…

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CNCTDiscriminator
Desktop

CNCTDiscriminator Coding and Non-coding Transcript Discriminator

A coding and noncoding transcript discriminating system where we applied the…

A coding and noncoding transcript discriminating system where we applied the integration of four categories of features about the transcripts: i) base compositions, (ii) ORF statistics, (iii)…

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Deeplnc
Web

Deeplnc

A web application for identifying long non-coding RNAs (lncRNAs). DeepLNC takes…

A web application for identifying long non-coding RNAs (lncRNAs). DeepLNC takes calibrated k-mer frequencies of lncRNAs and coding transcript sequences as its computational features. The k-mer…

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CPC
Web
Desktop

CPC Coding Potential Calculator

Distinguishes protein-coding from non-coding RNAs. CPC employs a discriminative…

Distinguishes protein-coding from non-coding RNAs. CPC employs a discriminative model based on four sequence intrinsic features. The CPC model is species-neutral, making it useful for ever-growing…

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lncRNA-MFDL
Desktop

lncRNA-MFDL

A powerful predictor to identify lncRNAs by fusing multiple features of the…

A powerful predictor to identify lncRNAs by fusing multiple features of the open reading frame, k-mer, the secondary structure and the most-like coding domain sequence and using deep learning…

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