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Permits functional annotation, management, and data mining of novel sequence data. Blast2GO is based on the utilization of common controlled vocabulary schemas, the gene ontology (GO). It takes in consideration similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations. This tool is suitable for plant genomics research. It generates functional annotation and assesses the functional meaning of their experimental results.


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 alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichment and more).

ST Pipeline

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 and identification of unique molecules. It is highly customizable with numerous parameter settings. The tool is more robust, efficient and scales better to arrays with higher density. It filters data, aligns it to a genome, annotates it to a reference, demultiplexes by array coordinates and then aggregates by counts that are not duplicates using the Unique Molecular Identifiers.


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 interface to characterize assembled transcript sequences and to initiate comparative genomics analyses. It enables scientists with a biological background to explore their non-model transcriptome data. The analysis process includes: the automatic identification of coding sequences in transcripts, correcting frameshifts, assigning coding-sequences to multi-species gene families, performing transcript quality control, and generating functional annotations.


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.


Provides comprehensive functional annotations. FunctionAnnotator is an annotation web-server that includes annotations for Gene Ontology (GO) terms, enzyme identification, domain detection, lipoprotein recognition, transmembrane domain discovery, subcellular localization annotation. It also provides the distribution of species from best hits at different taxonomic levels. It also discloses species distribution, functions for transcripts and all of the activated pathways hidden in the metatranscriptomic data.


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 and appears to be able to identify average 1000 proteins that were not annotated in the NCBI database. The tool appears to be complementary with MAKER-P for the identification of different genes: YeATSAM failed to annotate average 700 genes identified by MAKER-P, while identifying average 4000 genes missed by MAKER-P.

TRUFA / TRanscriptome User-Friendly Analysis

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 dynamically raw read cleaning, transcript assembly, annotation, and expression quantification. It uses highly parallelized steps to obtain annotations in a relatively short time frame. The software is essentially a wrapper of various widely used RNA-seq analysis tools, allowing the generation of RNA-seq outputs in an efficient, consistent, and user-friendly manner, based on a pipeline approach.

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

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 RNA-seq derived transcriptome sequences. YeATS unique feature is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts.

T-ACE / Transcriptome Analysis and Comparison Explorer

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. T-ACE offers a TCL-based interface, which accesses a PostgreSQL database via a php-script. Within T-ACE, information belonging to single sequences or contigs, such as annotation or read coverage, is linked to the respective sequence and immediately accessible. Sequences and assigned information can be searched via keyword- or BLAST-search. Additionally, T-ACE provides within and between transcriptome analysis modules on the level of expression, GO terms, KEGG pathways and protein domains.

Splicing Express

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 in an intuitive fashion. It is able to extract meaningful information from deep transcriptome data and performs statistical analysis aiming to give significance values to the fold differences between the splicing variants. The complete automation in Splicing Express makes it a useful tool for deep analysis of ASE in any transcriptome.


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 focusing on non-model organisms or metatranscriptomes. The tool integrates several well-developed annotation tools together to provide annotations for query sequences. It is capable of efficiently annotating sequences and is suitable for annotation of sequences derived from less well-studied organisms or environmental samples.


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 data; (2) determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3) assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4) generates output in HTML, text and GFF formats for the user's convenience.


Automatically maps and characterizes cDNAs. cDNA2Genome is an automated task for the high throughput mapping and annotation of cDNAs, using several frequently updated databases. The analysis programs used by cDNA2Genome can be divided into three main categories: database homology searches, gene finders, and sequence feature predictors. The use of standardized data formats like XML permits the use of the results in further analysis pipelines or their integration into databases.


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 referenced methods for (i) functional annotation including homology search to known sequence data (BLAST+/SwissProt), (ii) protein domain identification (HMMER/PFAM), (iii) protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and (iv) leveraging various annotation databases (eggNOG/GO/Kegg databases). This resource also includes TrinotateWeb, a locally-driven web-based graphical interface for navigating transcriptome annotations.


Assists users in selection of RNA targets. RiboSubstrates is a portable software that can be adapted to any kind of RNA silencing requirements, and may be used to scan any predefined cDNA database. The main goal of the program is to evaluate whether or not a given ribozyme sequence has a suitable and unique target sequence within the transcriptome of a particular genome. It allows identification of potential gene targets for SOFA-HDV ribozymes, hammerhead ribozymes and siRNAs.