Reference peptide dataset for HIV enveloppe

Description

A peptide dataset created from the multiple alignment of the reference sequence hxb2 and the seven subtypes A, B, C, D, M, CRF01, CRF02

Usage

data(pep_hxb2)

Format

A GRanges object. One row per peptide.

Details

• peptides: The rownames are 15mers from the envelope of 7 subtypes of HIV-1.

• 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 hxb2.

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

• trimmed: The trimmed column represents the part of hxb2's sequence aligned with the 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/HXB2.html

Results