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Extracts DNA sequences from biomedical articles and automatically maps them to genomic databases. text2genome links articles to genes and organisms without relying on gene names or identifiers. It also produces genome annotation tracks of the biomedical literature, thereby allowing researchers to use the power of modern genome browsers to access and analyze publications in the context of genomic data. System performance of the tool is related to the number of predictions made per paper.
Identifies potential name occurrences in the biomedical text and associate protein and gene database identifiers with the detected matches. ProMiner follows a rule-based approach and its search algorithm is geared towards recognition of multi-word names. It can be adapted to the characteristics of each organism using parameter settings and customized dictionary curation. The tool is able to obtain a high level of performance based on the classification of synonyms into several search classes.
Informatives extraction method for various natural language processing tasks including: supervised name entity recognition and relationship extraction from biomedical documents. rainbow-nlp is based on distributional semantic similarity over the Gene Ontology (GO) terms. With a focus on gene functions, it includes two subtasks: (i) retrieving GO evidence sentences for relevant genes and (ii) predicting GO terms for relevant genes. The main advantage of using unsupervised open-IE technique is that it can easily be generalized and applied to similar relation extraction problems.
GOCat / Gene Ontology Categorizer
Computes similarities between an input text and already curated instances contained in a knowledge base to infer gene ontology concepts. The main limit of GOCat, both observed by reviewers and mentioned in our papers, was the difficulty to integrate it in a curation workflow: it is stated that GOCat proposes more accurate (Gene Ontology) GO concepts, but these concepts are inferred from the whole abstract, then the curators still have to locate the function in the publication and to link the correct GO concept with a gene product.
PatSeq Analyzer
Offers a genome viewer dedicated to explore patenting activities of sequences of interest. PatSeq Analyzer is a web application, part of the PatSeq toolkit, that allows users to :(i) investigate specific patent sequences, refine mapping position, and make comparisons of patenting trends, from either recorded patent sequences mapped onto five different genome or personal files and to; (ii) search by gene or SEQ ID for analyzing or predicting patenting activities related to it.
PatSeq Explorer
Investigates biological sequences in patent documents. PatSeq Explorer allows users to explore patent-disclosed sequences on a genome of a specific organism as well as determine linkages between sequences and phenotypes. The application contains patent sequences mapped onto five different genome such as soybean and mouse. It includes multiple features for searching (by keywords, inventors or classification) and filtering (by years or sequence length) for assisting users in highlighting patenting trends. It is part of the PatSeq toolkit.
Enables the rapid identification of specific gene families of interest in related species. OrthoRBH streamlines the collection of homologs prior to downstream molecular evolutionary analysis. The efficacy of the program is demonstrated with the identification of the 13-member PYR/PYL/RCAR gene family in Hordeum vulgare using Oryza sativa query sequences. OrthoRBH is not recommended in situations where sequence homology is very low, for instance, identifying homologous sequences between plants and animals.
Provides several advanced functionalities in addition to the standard browsing capability of the official Gene Ontology (GO) browsing tool. DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations. The results are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. DynGO is generally applicable to any data set where the records are annotated with GO terms.
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PatSeq Data
Compiles data about patents disclosing genetic sequences. PatSeq Data is built around data collected from national patent offices, public sequence listings repositories or intellectual property organizations. Searches can be made by jurisdiction, document type, sequence type or location. The database provides additional statistics based on criteria, such as document or sequence type or data sources, as well as information about the public availability of sequences listings in the corresponding patent office. It is part of the PatSeq toolkit.
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