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 requiring efficient management of large datasets.
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.
Offers a component-based architecture that allows users to add new functionality in the form of plug-in modules. geWorkbench includes many computational resources permitting to delete many steps that require programming skills. It simplifies the utilization of multi-module analysis pipelines. The tool’s modules consist of wrapped versions of pre-existing third-party software tools.
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 obtain a better overview of their results. The software performs relatively small numbers of sequences in a single analysis, including the ability to parallelize search jobs to minimize wall-clock time.
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.
Enables access and manipulation of gene models and other annotations. GenomicFeatures is a set of tools and methods that allows to make and manipulate transcript centric annotations. The software provides an automated mechanism for constructing a TranscriptDb object from tracks defined in the UCSC genome browser, Biomart, or GTF/GFF files.
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).
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.