Literature DB >> 9283748

Linguistic approaches to biological sequences.

D B Searls1.   

Abstract

Biologists have long made use of linguistic metaphors in describing and naming cellular processes involving nucleic acid and protein sequences. Indeed, it is very natural to view the genetic 'text' and its sequential transliterations in these terms. However, a metaphor is not a tool, and it is necessary to ask whether the techniques used in analyzing other kinds of languages, such as human and computer languages, can in fact be of any use in tackling problems in molecular biology. This paper reviews the work of the author and others in applying the methods of computational linguistics to biological sequences.

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Year:  1997        PMID: 9283748     DOI: 10.1093/bioinformatics/13.4.333

Source DB:  PubMed          Journal:  Comput Appl Biosci        ISSN: 0266-7061


  14 in total

1.  Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis.

Authors:  H J Bussemaker; H Li; E D Siggia
Journal:  Proc Natl Acad Sci U S A       Date:  2000-08-29       Impact factor: 11.205

2.  Aligning sequences by minimum description length.

Authors:  John S Conery
Journal:  EURASIP J Bioinform Syst Biol       Date:  2007

3.  Computational reasoning across multiple models.

Authors:  Guy Tsafnat; Enrico W Coiera
Journal:  J Am Med Inform Assoc       Date:  2009-08-28       Impact factor: 4.497

4.  A composite method based on formal grammar and DNA structural features in detecting human polymerase II promoter region.

Authors:  Sutapa Datta; Subhasis Mukhopadhyay
Journal:  PLoS One       Date:  2013-02-20       Impact factor: 3.240

5.  Duplicate gene enrichment and expression pattern diversification in multicellularity.

Authors:  Timothy Padawer; Ralph E Leighty; Degeng Wang
Journal:  Nucleic Acids Res       Date:  2012-05-29       Impact factor: 16.971

6.  A formal language-based approach in biology.

Authors:  Marian Gheorghe; Victor Mitrana
Journal:  Comp Funct Genomics       Date:  2004

7.  A grammar inference approach for predicting kinase specific phosphorylation sites.

Authors:  Sutapa Datta; Subhasis Mukhopadhyay
Journal:  PLoS One       Date:  2015-04-17       Impact factor: 3.240

8.  Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.

Authors:  Yizhi Cai; Matthew W Lux; Laura Adam; Jean Peccoud
Journal:  PLoS Comput Biol       Date:  2009-10-09       Impact factor: 4.475

9.  Word decoding of protein amino Acid sequences with availability analysis: a linguistic approach.

Authors:  Kenta Motomura; Tomohiro Fujita; Motosuke Tsutsumi; Satsuki Kikuzato; Morikazu Nakamura; Joji M Otaki
Journal:  PLoS One       Date:  2012-11-21       Impact factor: 3.240

10.  Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.

Authors:  Jens Reeder; Robert Giegerich
Journal:  BMC Bioinformatics       Date:  2004-08-04       Impact factor: 3.169

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