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Transcriptome annotation software tools | RNA sequencing data analysis

RNA-Seq has effectively portrayed the transcriptional complexity in eukaryotes demonstrating the widespread transcription of lncRNAs in a diverse group of organisms. However, annotation of de-novo generated transcriptomes, remains a complex task…
Blast2GO
Desktop

Blast2GO

A comprehensive bioinformatics tool for functional annotation of sequences and…

A comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes…

G T A T C G C T A
InterProScan
Desktop
Web

InterProScan

Scans sequences against InterPro's signatures. InterProScan allows users…

Scans sequences against InterPro's signatures. InterProScan allows users to characterize a nucleotide or protein function by matching it with models from several different databases and to…

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AltAnalyze
Desktop

AltAnalyze

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis.…

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess…

Pse-Analysis
Desktop

Pse-Analysis

Expedites the pace in conducting genome/proteome analysis. Pse-Analysis can…

Expedites the pace in conducting genome/proteome analysis. Pse-Analysis can automatically complete the following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3)…

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spliceR
Desktop

spliceR

Sorts alternative splicing (AS) and discovers coding potential. spliceR…

Sorts alternative splicing (AS) and discovers coding potential. spliceR simplifies downstream sequence analysis by allowing annotation of genomic coordinates of the differentially spliced elements.…

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ST Pipeline
Desktop

ST Pipeline

Permits to process and analyze the raw files generated with the Spatial…

Permits to process and analyze the raw files generated with the Spatial Transcriptomics (ST) method. ST Pipeline enables demultiplexing of spatially-resolved RNA-seq data and robust quality filtering…

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FIT
Desktop

FIT

Offers functions for parameter optimization and transcriptome prediction. FIT…

Offers functions for parameter optimization and transcriptome prediction. FIT achieves comparable or better prediction performance within a shorter computational time than the previous method. It…

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sim4cc
Desktop

sim4cc

A heuristic sequence alignment tool for comparing a cDNA sequence with a…

A heuristic sequence alignment tool for comparing a cDNA sequence with a genomic sequence containing a homolog of the gene in another species. sim4cc is built on the foundation of sim4 and…

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Annocript
Desktop

Annocript

Combines the annotation of protein coding transcripts with the prediction of…

Combines the annotation of protein coding transcripts with the prediction of putative lncRNAs in whole transcriptomes. Annocript downloads and indexes the needed databases, runs the analysis and…

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systemPipeR
Desktop

systemPipeR

An extensible environment for both building and running end-to-end analysis…

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…

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TRAPID
Web

TRAPID

Allows users to process transcriptomes from animals, plants, fungi, and…

Allows users to process transcriptomes from animals, plants, fungi, and bacteria. TRAPID is a web and high-throughput analysis application using predefined reference databases. It offers an online…

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FunctionAnnotat…
Web

FunctionAnnotator

Provides comprehensive functional annotations. FunctionAnnotator is an…

Provides comprehensive functional annotations. FunctionAnnotator is an annotation web-server that includes annotations for Gene Ontology (GO) terms, enzyme identification, domain detection,…

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PhysalisDB
Dataset

PhysalisDB

Offers access to annotations and secondary data generated for Physalis…

Offers access to annotations and secondary data generated for Physalis peruviana that are not published in the main biological databases. PhysalisDB is an online resource tightly integrated with…

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TRUFA
Web

TRUFA TRanscriptome User-Friendly Analysis

Offers a web-based interface that generates the outputs commonly used in de…

Offers a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing…

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TCW
Desktop

TCW Transcriptome Computational Workbench

A software package for assembling, annotating, querying, and comparing…

A software package for assembling, annotating, querying, and comparing transcript and expression level data.

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Transcriptator
Web

Transcriptator

Translates transcriptomics data from RNA-seq or micro-array experiments into…

Translates transcriptomics data from RNA-seq or micro-array experiments into biological interpretations. Transcriptator allows users to annotate the assembled reads dataset obtained from RNA-seq…

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YeATSAM
Desktop

YeATSAM

Annotates genome by using information encoded by the transcriptome. YeATSAM…

Annotates genome by using information encoded by the transcriptome. YeATSAM splits the assembled transcriptome into multiple open reading frames (ORFs). It was tested on the chickpea transcriptome…

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Splicing…
Desktop

Splicing Express

Provides a simple and effective way for the identification, annotation and…

Provides a simple and effective way for the identification, annotation and visualization of Alternative Splicing Events (ASEs). Splicing Express is a software suite that provides expression graphics…

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CAT
Desktop

CAT Cross-species Alignment Tool

Aligns mRNA sequences to mammalian-sized genomes. CAT is designed to be a…

Aligns mRNA sequences to mammalian-sized genomes. CAT is designed to be a cross-species cDNA-to-genome alignment software. This algorithm was developed to combine the specificity of the intra-species…

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YeATS
Desktop

YeATS Yet Another Tool Suite for analyzing RNA-seq derived transcriptome

A methodology that replicates and improves existing methodologies, and…

A methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for…

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T-ACE
Desktop

T-ACE Transcriptome Analysis and Comparison Explorer

A tool designed for the organization and analysis of large sequence datasets,…

A tool designed for the organization and analysis of large sequence datasets, and especially suited for transcriptome projects of non-model organisms with little or no a priori sequence information.…

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FastAnnotator
Web

FastAnnotator

Assigns functional annotations. FastAnnotator efficiently annotates sequences…

Assigns functional annotations. FastAnnotator efficiently annotates sequences with their gene functions, enzyme functions or domains. It is useful in transcriptome studies and especially for those…

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annot8r
Desktop

annot8r

A tool that assigns GO, EC and KEGG annotations for data sets resulting from…

A tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and…

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AutoFACT
Desktop

AutoFACT

A fully automated and customizable annotation tool that assigns biologically…

A fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1) analyzes nucleotide and protein sequence…

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GOtcha
Desktop
Web

GOtcha

A method for predicting gene product function by annotation with Gene Ontology…

A method for predicting gene product function by annotation with Gene Ontology (GO) terms. GOtcha predicts GO term associations with term-specific probability (P-score) measures of confidence. GOtcha…

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Trinotate
Desktop

Trinotate

Helps for automatic functional annotation of transcriptomes, especially de novo…

Helps for automatic functional annotation of transcriptomes, especially de novo assembled transcriptomes. Trinotate is an annotation suite developed that makes use of a number of different well…

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