Results for "Annotation"



    MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-ini...

    Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, MAKER, Genome, Annotation, Pipeline, NGS, Assembly

    676 days ago


    Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at

    Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, BUSCO, Genome, Annotation, Pipeline, NGS, Assembly, Orthologs

    676 days ago

  • RATT

    RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome. It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between strains and even different species, like Plasmo...

    Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, RATT, Genome, Annotation, Pipeline, NGS, Assembly

    676 days ago

  • flo

    flo - same species annotations lift over pipeline Lift over is the process of transferring annotations from one genome assembly to another. Usually lift over is done because there is a new, improved genome assembly for the species and good quality annotations (maybe manually curated or experimen...

    Tags: Bioinformatics, Flo, Liftover, Annotation

    673 days ago

  • NCBI Remap

    NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use the API for NCBI Remap. More at http://www.ncbi...

    Tags: Bioinformatics, NCBI, NCBI Remap, Liftover, Annotation

    672 days ago

  • Centurion

    Although centromeres are essential for life and are the subject of extensive research, centromere locations in yeast genomes are difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation assay Hi-C has been re-purposed for diverse applications, including...

    Tags: Bioinformatics, Centromere, Centurion, HiC, Annotation

    672 days ago

  • HiCdat

    HiCdat: a fast and easy-to-use Hi-C data analysis tool HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic featu...

    Tags: Bioinformatics, HiC, Analysis, HiCdat, Annotation

    672 days ago

  • RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently...

    Tags: Bioinformatics, NGS, Tk, Pipeline, Annotation, Tool, RASTtk

    596 days ago

  • GeneMANIA

    Faster, more accurate algorithms function prediction "GeneMANIA (Multiple Association Network Integration Algorithm)" have however been developed in recent years and are publicly available on the web, indicating the future direction of function prediction.

    Tags: Bioinformatics, Analysis, NGS, Annotation, Genome

    479 days ago


    Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervis...

    Tags: Bioinformatics, Analysis, NGS, Braker, Annotation, Genes, Predictions, Genome

    470 days ago