Geodesic
Category theory for genetics I:mutations and sequence alignments
Theory and applications of categories, Tome 33 (2018), pp. 1269-1317

Voir la notice de l'article provenant de la source Theory and Applications of Categories website

The present article is the first of a series whose goal is to define a logical formalism in which it is possible to reason about genetics. In this paper, we introduce the main concepts of our language whose domain of discourse consists of a class of limit-sketches and their associated models. While our program will aim to show that different phenomena of genetics can be modeled by changing the category in which the models take their values, in this paper, we study models in the category of sets to capture mutation mechanisms such as insertions, deletions, substitutions, duplications and inversions. We show how the proposed formalism can be used for constructing multiple sequence alignments with an emphasis on mutation mechanisms.

Publié le :
Classification : 18C99, 92B99
Keywords: Multiple sequence alignment, mutation mechanism, right Kan extension, category, limit sketch, pedigrad 
@article{TAC_2018_33_a39,
     author = {Remy Tuyeras},
     title = {Category theory for genetics {I:mutations} and sequence alignments},
     journal = {Theory and applications of categories},
     pages = {1269--1317},
     publisher = {mathdoc},
     volume = {33},
     year = {2018},
     language = {en},
     url = {http://geodesic.mathdoc.fr/item/TAC_2018_33_a39/}
}
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Remy Tuyeras. Category theory for genetics I:mutations and sequence alignments. Theory and applications of categories, Tome 33 (2018), pp. 1269-1317. http://geodesic.mathdoc.fr/item/TAC_2018_33_a39/