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

[Simon Penel]

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:
http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-5.pdf

User level visible changes are:

o  A  new function dotPlot() is now available.
   
http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/dotPlot.html

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.

http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/crelistfromclientdata.html 


o  A new function pmw() to compute the molecular weight of a protein is now
   available.
   http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/pmw.html

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.

http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/reverse.align.html 


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.
   http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/uco.html

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 
read.table()
   or scan(), the file argument starts now with a lower case letter 
(i.e."file")
   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.

http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/read.fasta.html 


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

http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/write.fasta.html 


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.
   http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/kaks.html

all the best,

Simon

-- 
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
http://pbil.univ-lyon1.fr/members/penel

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