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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).
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] In 2015, a group reviewed the different kinds of analyses and tools a researcher may have available. [55]
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.
seq2HLA is an annotation tool for obtaining an individual's HLA class I and II type and expression using standard NGS RNA-Seq data in fastq format. It comprises mapping RNA-Seq reads against a reference database of HLA alleles using bowtie, determining and reporting HLA type, confidence score and locus-specific expression level.
REAL is an efficient, accurate, and sensitive tool for aligning short reads obtained from next-generation sequencing. The programme can handle an enormous amount of single-end reads generated by the next-generation Illumina/Solexa Genome Analyzer. cREAL is a simple extension of REAL for aligning short reads obtained from next-generation ...
The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
Faster and efficient tools are needed to keep pace with the high-throughput sequencing, because the BLAST-based approaches such as MG-RAST or MEGAN run slowly to annotate large samples (e.g., several hours to process a small/medium size dataset/sample [56]). Thus, ultra-fast classifiers have recently emerged, thanks to more affordable powerful ...
A metabolic reconstruction provides a highly mathematical, structured platform on which to understand the systems biology of metabolic pathways within an organism. [2] The integration of biochemical metabolic pathways with rapidly available, annotated genome sequences has developed what are called genome-scale metabolic models.