[Seqinr-forum] changes in 1.1-7

[Jean lobry]

Dear seqinr,

release 1.1-7 is now on its way to CRAN. A summary of changes is below.

Best,

Z.


o As suggested by Kurt Hornik two extra 'cr' in the
   documentation file for ec999 were deleted.

o Function read.fasta() has gained four new arguments
   (viz. bfa, sizeof.longlong, endian, apply.mask) to read DNA binary fasta
   files in MAQ format. There is a new ct.bfa file
   in the sequences folder to check for the MAQ format
   reading.

o New dataset pK for the values for the side chain of
   charged amino acids from various sources compiled by Joanna Kiraga
   \cite{KiragaJ2008}.

o Function words.pos() has gained new arguments that
   are passed to regexpr() including the dot-dot-dot
   argument in case of need in the future. The documentation has
   been modified to better explain the difference with the standard
   gregexpr() function.

o As pointed by e-mail on 28 May 2008 by Kim Milferstedt a
   function to compute the consensus for a set of aligned sequences
   would be helpful. There is now a function consensus()
   aliased to con() for this. The input is either an object
   from class alignment or a matrix of characters. The
   output is either a consensus sequence (using the majority rule,
   the majority rule with a threshold, or IUPAC symbols for RNA
   and DNA sequences) or a profile, that is a matrix with the count
   of each possible character at each position in the alignment.

o In the documentation of the read.alignment() function
   a link was added to the read.nexus() function from the
   ComPairWise package \cite{ComPairWise}.

o New function bma() to find the IUPAC symbol corresponding
   to a nucleic sequence.

o New function as.matrix.alignment() to convert an
   alignment into a object of class matrix.

o The encoding of line ends in the example file test.mase
   is now an unix-like one.

o As pointed by e-mail on 31 May 2008 by Marie Sémon there was
   no convenient function to compute the Codon Adaptation Index \cite{CAI}.
   A new function cai() was introduced with the aim of reproducing
   exactly the results from the program codonW that was written
   by John Peden during his PhD thesis \cite{codonW} under the supervision
   of P.M. Sharp (the most authorative source for CAI computation). A new
   dataset caitab that was hard-encoded in codonW for
   the w values for some species (viz Escherichia coli, Bacillus subtilis,
   Saccharomyces cerevisiae) was added. Care was taken to credit
   original sources. The E. coli data that was uncredited is
   from \cite{CAI}. The B. subtilis data that was uncredited
   is from \cite{ShieldsDC1987} (see the note of caution in ?caitab
   before using this one directly to compute CAI in B. subtilis).
   The S. cerevisiae data that was credited to \cite{SharpPM1991}
   dates back from \cite{CAI}. A new text file scuco.txt produced by codonW
   was added in the sequences folder to check that the CAI results from
   cai() are consistents with thoses from codonW version
   1.4.4 (03-MAR-2005). This legacy file is used in the example section of
   the cai() function.

References:
-----------

@PhDThesis{KiragaJ2008,
    Author = {Kiraga, J.},
    Title = {Analysis and computer simulations of variability of 
isoelectric point of proteins in the proteomes.},
    School = {University of Wroc{\l}aw},
    Year = {2008}
}

@Manual{ComPairWise,
     title = {ComPairWise: Compare phylogenetic or population genetic 
data alignments},
     author = {Trina E. Roberts},
     year = {2007},
     note = {R package version 1.01},
}

@article{CAI,
    Author = {Sharp, P.M. and Li, W.-H.},
    Title = {The codon adaptation index - a measure of directional 
synonymous codon usage bias,
      and its potential applications},
    Journal = {Nucleic Acids Research},
    Volume = {15},
    Pages = {1281-1295},
  Year = {1987}
}

@PhDThesis{codonW,
    Author = {Peden, J.F.},
    Title = {Analysis of codon usage},
    School = {University of Nottingham},
    Year = {1999}
}

@article{ShieldsDC1987,
    Author = {Shields, D.C. and Sharp, P.M.},
    Title = {Synonymous codon usage in \textit{Bacillus subtilis}
   reflects both translational selection and mutational biases},
    Journal = {Nucleic Acids Research},
    Volume = {15},
    Pages = {8023-8040},
  Year = {1987} }

@article{SharpPM1991,
    Author = {Sharp, P.M. and Cowe, E.},
    Title = {Synonymous codon usage in \textit{Saccharomyces cerevisiae}},
    Journal = {Yeast},
    Volume = {7},
    Pages = {657-678},
  Year = {1991} }
-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo  : +33 472 43 27 56     fax    : +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/