The seqinR package for the R environment is a library of utilities to retrieve and analyze biological sequences. It provides an interface between: (i) the R language and environment for statistical computing and graphics, and (ii) the ACNUC sequence retrieval system for nucleotide and protein sequence databases such as GenBank, EMBL, SWISS-PROT. ACNUC is very efficient in providing direct access to subsequences of biological interest (e.g., protein coding regions, tRNA, or rRNA coding regions) present in GenBank and in EMBL. Thanks to a simple query language, it is then easy under R to select sequences of interest and then use all the power of the R environment to analyze them. The ACNUC databases can be locally installed but they are more conveniently accessed through a web server to take advantage of centralized daily updates. The aim of this chapter is to provide a handout on basic sequence analyses under seqinR with a special focus on multivariate methods.
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Charif, D., Lobry, J.R. (2007). SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis. In: Bastolla, U., Porto, M., Roman, H.E., Vendruscolo, M. (eds) Structural Approaches to Sequence Evolution. Biological and Medical Physics, Biomedical Engineering. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-35306-5_10
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