[R] [R-pkgs] seqinr updated : release 1.0-5

From: Simon Penel <penel_at_biomserv.univ-lyon1.fr>
Date: Tue 25 Jul 2006 - 22:25:12 EST

Dear R users,

seqinR 1.0-5 has been released yesterday on CRAN, so that the source code of the package should be available on all CRAN mirrors within the next 24h.

The updated package vignette is here:

User level visible changes are:

o A new function dotPlot() is now available.    


o A new function crelistfromclientdata() is now available to create a list on

   the server from a local file of sequence names, sequence accession numbers,

   species names, or keywords names.


o A new function pmw() to compute the molecular weight of a protein is now


o A new function reverse.align() contributed by Anamaria Necsulea is now

   available to align CDS at the protein level and then reverse translate    this at the nucleic acid level from a clustalw output. This can be done    on the fly if clustalw is available on your platform.


o An undocumented behavior was reported by Guy Perriere for uco() when

   computing RSCU on sequences where an amino-acid is missing. There is    now a new argument NA.rscu that allows the user to force the missing    values to his favorite magic value.

o There was a bug in read.fasta(): some sequence names were truncated, this

   is now fixed (thanks to Marcus G. Daniels for pointing this).    In order to be more consistent with standard functions such as

   or scan(), the file argument starts now with a lower case letter 

   in function read.fasta(), but the old-style "File" is still functional for

   forward-compatibility. There is a new logical argument in read.fasta()    named as.string to allow sequences to be returned as strings instead of    vector of single characters. The automatic conversion of DNA sequences into

   lower case letters can now be disabled with the new logical argument    forceDNAtolower. It is also possible to disable the automatic attributes    settings with the new logical argument set.attributes.


o A new function write.fasta() is now available.


o The function kaks() now forces character in sequences to upper case.

   This default behavior can be neutralized in order to save time by setting the

   argument forceUpperCase to FALSE.

all the best,


Simon Penel
Laboratoire de Biometrie et Biologie Evolutive           
Bat 711  -   CNRS UMR 5558  -    Universite Lyon 1              
43 bd du 11 novembre 1918 69622 Villeurbanne Cedex       
Tel:   04 72 43 29 04      Fax:  04 72 43 13 88

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Received on Wed Jul 26 01:14:30 2006

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