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MG-RAST, an open-source web application server, facilitates automatic phylogenetic and functional analysis of metagenomes.It stands as one of the largest repositories for metagenomic data, employing the acronym for Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST).
BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weights, isoelectric points, operon structures, subcellular localization, signal peptides, transmembrane regions ...
This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics , cladistics , and bioinformatics .
Manual image annotation is the process of manually defining regions in an image and creating a textual description of those regions. Such annotations can for instance be used to train machine learning algorithms for computer vision applications. This is a list of computer software which can be used for manual annotation of images.
As interest in pangenomes increased, there have been several software tools developed to help analyze this kind of data. To start a pangenomic analysis the first step is the homogenization of genome annotation. [23] The same software should be used to annotate all genomes used, such as GeneMark [53] or RAST. [54]
UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing. SpliceTrap [77] is a statistical tool for the quantification of exon inclusion ratios from RNA-seq data. Splicing Express – a software suite for alternative splicing analysis using next-generation sequencing data.
Software by Bruker used with mass spectrometry instruments. DeNovoGUI Open source: The software has a graphical user interface for running parallelized versions of the freely available de novo sequencing software tools Novor and PepNovo+. [51] Easotope Open source: Easotope software archives, organizes, and analyzes mass spectrometer data.
The ANNOVAR software accepts text-based input files, including VCF (Variant Call Format), the gold standard for describing genetic loci. The program's main annotation script, annotate_variation.pl requires a custom input file format, the ANNOVAR input format (.avinput). Common file types can be converted to ANNOVAR input format for annotation ...