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MutationFinder specifications


Unique identifier OMICS_09111
Name MutationFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Perl, Python
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for MutationFinder

MutationFinder citations


nala: text mining natural language mutation mentions

PMCID: 5870606
PMID: 28200120
DOI: 10.1093/bioinformatics/btx083

[…] y in their syntax: the first is written in natural language (NL), the second follows a standardized format (ST).Existing extraction methods primarily target simple and standardized mutation mentions. MutationFinder (MF) (,) uses a large set of regular expressions (regexes) to recognize single nucleotide or amino acid variants written in simple ST form (e.g. ‘E6V’) and slightly more complex semi-st […]


Text Mining Genotype Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine

PLoS Comput Biol
PMCID: 5130168
PMID: 27902695
DOI: 10.1371/journal.pcbi.1005017

[…] s confine their scope to mutation entity extraction without exploring the relationships of those mutations to other entities, such as diseases or genes. Examples of mutation recognition tools include MutationFinder [], tmVar [], and several others [].Several groups, however, have addressed variant relationship mining in text. One early, notable method developed by Kuipers et al [] introduced an au […]


Establishing a baseline for literature mining human genetic variants and their relationships to disease cohorts

BMC Med Inform Decis Mak
PMCID: 4959367
PMID: 27454860
DOI: 10.1186/s12911-016-0294-3

[…] A recent survey of biomedical corpora [] identifies only a small number of corpora related to genetic variation specifically, including the corpora focused on singular nucleotide polymorphisms (MutationFinder [], the SNPCorpus []), and corpora considering a somewhat broader spectrum of biological sequence information (the OSIRIS corpus [], and Nagel corpus []).There are even fewer corpora th […]


Mutation extraction tools can be combined for robust recognition of genetic variants in the literature

PMCID: 4176422
PMID: 25285203
DOI: 10.5256/f1000research.3422.r3233

[…] letion ( c.2700_2701delTC). EMU false negatives include deletions c.3927_3931del AAAGA, substitutions such as c.1852_1853AA>GC and mentions surrounded by parentheses. Considering the false negatives, MutationFinder failed at extracting mutations with three-letter amino acids (e.g., p.Pro622Thr) or single-letter amino acids without the p. prefix as M23A. OMM has only two false negatives that are pr […]


An analysis on the entity annotations in biological corpora

PMCID: 4168744
PMID: 25254099
DOI: 10.5256/f1000research.3456.r4561

[…] nzymes corpus contains annotations for metabolites and enzymes names in almost 300 abstracts and was used for the evaluation of dictionary-based approaches for the recognition of these entity types. MutationFinder. The MutationFinder corpus is composed of 508 Medline abstracts annotated with mutations and it was used for the evaluation of the homonymous tool based on regular expression technique […]


Benchmarking infrastructure for mutation text mining

J Biomed Semantics
PMCID: 3939821
PMID: 24568600
DOI: 10.1186/2041-1480-5-11

[…] We retrieved 201 documents annotated with singular amino acid substitutions grounded to proteins, from the KinMutBase [] database. We additionally curated the selection by running MutationFinder [], which is a reliable tool for this purpose due to its very high recall, and comparing the results with the annotations in the database. Based on this comparison, we discarded about 7 […]

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MutationFinder institution(s)
University of Colorado Health Sciences Center, Aurora, CO; Motorola Mobile Devices, Libertyville, IL; Department of Computer Science; Department of Linguistics, University of Colorado at Boulder, Boulder, CO, USA

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