Search Results for "sequence ontology"

... for the entire scaffold, taking into account the taxonomic ontology. Scaffolds that exclusively match potential contaminants may be safely removed while sequences matching partially contaminants and partially the target organism may constitute horizontal transfers or assembly artifacts and need to be examined manually.

Make it SO. This aim of this project is to develop both an ontology and a set of software modules to be used to describe and communicate biological sequence information.

mx is a Ruby/Rails code base with broad application in evolutionary biology, it includes general functionality for matrix handling, sequence management, ontology construction, specimen handling, taxonomic catalogs, taxonomic descriptions and more

ASOoViR is a set of Ruby modules to annotate consequence terms, defined by the Sequence Ontology, of variants (SNP/SNVs, INDELs, SVs, CNAs) using Ensembl gene sets. Prior to annotation of variants an Ensembl gene set and reference coding sequences are loaded into memory from a database file, which can be downloaded or generated by the user from reference files. This allows rapid annotation of variants, making it suitable for annotation of whole genome scale calls. Annotation is performed...

A interpreter based on semantic web. A sequence of relation-word combination in an input text file is matched against a pattern text file and executes a simple macro language. The pattern is based on a given ontology.

Danaides stores meta-data from biological banks in a graph databases as well as OBO formatted ontologies. It also provides a web query interface to parse ontologies or extract nodes based on ontology requirements. Example: Get all known elements that are in family of Fish (species ontology) AND a RNA (sequence ontology).