Results for "Annotation"
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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
2999 days ago
- Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/
Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, BUSCO, Genome, Annotation, Pipeline, NGS, Assembly, Orthologs
2999 days ago
- 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
2999 days ago
- 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
2996 days ago
- 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
2995 days ago
- 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
2994 days ago
- 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
2994 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
2919 days ago
- 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
2802 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
1940 days ago
