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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