SeqinR
Seqinr : Biological Sequences in R
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The seqinR package for the R environment is a library of utilities to retrieve and analyse biological sequences. It provides an interface between:
  1. the R language and environment for statistical computing and graphics and
  2. the ACNUC (Gouy et al., 1985) 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.

seqinr is now available on R-forge: https://r-forge.r-project.org/projects/seqinr/