maChain: maChain

In mskilab/gChain: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

maChain

Description

Multiple sequence alignment chain

Takes input GRangesList of interval coordinates corresponding to sequences contributing to alignments in pali. 'pali' is a list of alignment matrices (containing letters from the original sequences and '-', '.' for gaps)

'grl' and 'pali', have the same names (corresponding to the alignment, e.g. a protein domain) Also, this property holds: sapply(pali, nrow) = sapply(grl, length)

trim will remove all alignment columns that have only gaps

alternatively, grl can be an XStringSet object with a "names" attribute containing Biostrings (eg AA or DNA) and gap ("-") characters. Can also be a list of XStringSet objects.

if grl is NULL, then it is assumed that the first (last) non gapped character in each MSA alignment entry represents the first (last) item of the sequence

Usage

maChain(grl = NULL, pali, pad = 0, trim = TRUE, trim.thresh = 0, ...)

Author(s)

Marcin Imielinski

mskilab/gChain documentation built on Sept. 28, 2022, 3:45 p.m.