ptm (version 0.2.2)

custom.aln: Download and Align Orthologous Sequences

Description

Downloads orthologous sequences and carries out their alignment

Usage

custom.aln(target, species, molecule = 'protein', sfile = FALSE)

Arguments

target

the KEGG identifier of the protein of interest.

species

a character vector containing the KEGG code for the species of interest.

molecule

a character string specifying the nature of the sequence; it must be one of 'dna', 'protein'.

sfile

logical, if TRUE the alignment in fasta format is saved in the current directory.

Value

Returns a list of class "fasta" with three components: 'ali' (an alignment character matrix with a row per sequence and a column per residue), 'id' (sequence identifiers) and 'call' (the matched call).

Details

We can build the list of species or, alternatively, we can choose between four pre-established options: 'vertebrates', 'plants','one-hundred' and 'two-hundred'. The first will use the following seven species: human (hsa), chimp (ptr), gorilla (ggo), rat (rno), cow (bta), chicken (gga), western clawed frog (xtr) and zebrafish (dre). The second, A. thaliana (ara), A. lyrata (aly), B. oleracea (boe), G. max (gmax), S. lycopersicum (sly), O. sativa (osa) and C. reinhardtii (cre). The third and fourth options will use orthologous sequences from one hundred and two hundred different species, respectively.

References

Edgar RC. Nucl. Ac. Res. 2004 32:1792-1797.

Edgar RC. BMC Bioinformatics 5(1):113.

See Also

msa(), list.hom(), parse.hssp(), get.hssp(), shannon()

Examples

# NOT RUN {
custom.aln('hsa:4069', species = c('pps', 'pon', 'mcc', 'ssc'))
# }
# NOT RUN {
custom.aln('cge:100773737', 'vertebrates', molecule = 'dna' )
# }