SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis

The seqinR package for the R environment is a library of utilities to retrieve and analyse 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 paper is to provide a handout on basic sequence analyses under seqinR with a special focus on multivariate methods.

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