Reference peptide dataset for SIV enveloppe

Description

A peptide dataset created from the multiple alignment of the reference sequence mac239 from LANL database, our mac239 and E660 subtypes.

Usage

data(pep_mac239)

Format

A GRanges object. One row per peptide.

Details

• peptides: The rownames are 15mers from the envelope of mac239 and E660.

• seqnames: An information regarding the genomic location of the peptide.

• ranges: The start and end coordinate of the peptide based on the coordinates of the reference mac239.

• aligned: The aligned column represents the peptide as it is aligned in the multiple alignment.

• peptideNb:Number of the corresponding mac239 peptide.

• zSums: The sum of the zScale of each amino-acid of the 15mer.

• clade: A list of the subtypes which contain this peptide.

Note

The alignments used to create this collections are available in the extdata/alignments folder, as well as the raw sequences on fasta format.

References

http://www.hiv.lanl.gov/content/sequence/HIV/REVIEWS/SIV_NUMBERING2001/SivNumbering.html

Results