PRABI
Rhone-Alpes Bioinformatics Center


PRABI : LBBE

seqinR

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 (Gouy et al., 1985) sequence retrieval system for nucleotide and protein sequence databases such as GenBank, EMBL, SWISS-PROT, HOBACGEN and other HO*, ... .

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.

A complete documentation is available on the webpage with many examples.

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