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Mutation recognition software tools and databases | Bio-entity identification

Text-mining mutation information from the literature becomes a critical part of the bioinformatics approach for the analysis and interpretation of sequence variations in complex diseases in the post-genomic era. It has also been used for assisting…
nala
Desktop

nala

Allows extraction of sequence variants. nala is a text mining method designed…

Allows extraction of sequence variants. nala is a text mining method designed to handles natural Language (NL) and target standard (ST) mentions. The nala method and corpus, which is part of IDP4+,…

BioNLP
Desktop

BioNLP

Uses to create and distribute code, software, and data for applying natural…

Uses to create and distribute code, software, and data for applying natural language processing techniques to biomedical texts. The aim of BioNLP is to provide algorithms and knowledge-based tools…

SETH
Desktop

SETH SNP Extraction Tool for Human Variations

A tool for the recognition of variations from text and their subsequent…

A tool for the recognition of variations from text and their subsequent normalization to dbSNP or UniProt. SETH achieves high precision and recall on several evaluation corpora of PubMed abstracts.…

hivmut
Dataset

hivmut HIV Mutation

A database of mutagenesis and mutation information on Human Immunodefiency…

A database of mutagenesis and mutation information on Human Immunodefiency Virus (HIV). Hivmut describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from…

DiMeX
Dataset

DiMeX eXtraction of Mutation association to Diseases

A text mining system for mutation-disease association extraction. DiMeX…

A text mining system for mutation-disease association extraction. DiMeX consists of a series of natural language processing modules that preprocess input text and apply syntactic and semantic…

MRRAD
Dataset

MRRAD Multilingual Radiology Research Articles Dataset

Provides a corpus of Portuguese research articles about Radiology and human,…

Provides a corpus of Portuguese research articles about Radiology and human, automatic and semi-automatic translations to English. MRRAD containing for each article the original Portuguese document,…

TEPAPA
Desktop
MITOCLASS.1
Desktop

MITOCLASS.1

Classifies mtDNA missense variants. MITOCLASS.1 has performed better than other…

Classifies mtDNA missense variants. MITOCLASS.1 has performed better than other web-available tested predictors. It allows a better selection of candidate damaging missense variants from mtDNA. The…

MuGeX
Web

MuGeX Mutation Gene eXtractor

Automatically extracts mutation-gene pairs from MEDLINE abstracts for a given…

Automatically extracts mutation-gene pairs from MEDLINE abstracts for a given disease. With automatic extraction techniques, MuGeX overcomes the problems of information retrieval from public…

MEMA
Dataset

MEMA

Automates the detection of mutations and the extraction of mutation–gene…

Automates the detection of mutations and the extraction of mutation–gene pairs. The result is a database of such pairs. MEMA identified 24 351 singleton mutations in conjunction with a HUGO gene…

tmVar
Desktop

tmVar

Aims users to normalize and extract variant mentions to unique identifiers…

Aims users to normalize and extract variant mentions to unique identifiers (dbSNP RSIDs). tmVar is a method allowing analysis and integration of text-mined variant data in several databases. It…

MutD
Desktop

MutD

A text mining system which extracts protein mutation-disease associations from…

A text mining system which extracts protein mutation-disease associations from MEDLINE abstracts by incorporating discourse level analysis, using a benchmark data set extracted from curated database…

EMU
Desktop

EMU Extractor of MUtations

A high-throughput computational method for the identification of relevant…

A high-throughput computational method for the identification of relevant disease mutations in PubMed abstracts applied to prostate (PCa) and breast cancer (BCa) mutations. EMU identifies mutations…

MutationFinder
Desktop

MutationFinder

An open-source, rule-based system for extracting point mutation mentions from…

An open-source, rule-based system for extracting point mutation mentions from text. On blind test data, MutationFinder achieves nearly perfect precision and a markedly improved recall over a…

MuteXt
Desktop

MuteXt

A computational method that identifies and extracts mutation data from the…

A computational method that identifies and extracts mutation data from the scientific literature. The efficiency of MuteXt is consistent across these two well-studied families and relies on the…

EnzyMiner
Web

EnzyMiner

Automatically identifies the PubMed abstracts that contain information on the…

Automatically identifies the PubMed abstracts that contain information on the impact of a protein level mutation on the stability or the activity of a given enzyme. For querying EnzyMiner, please…

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