codon.clean.msa: Clean an alignment for codon analysis
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Clean an alignment for codon analysis

1	codon.clean.msa(x, refseq = NULL, strand = "+")

`x`	An object of type `msa`
`refseq`	The name of the reference sequence to be used. If given, strip all columns which contain gaps in refseq. Once this is done, alignment should be in frame. If `refseq==NULL` then alignment should be in frame as it is sent in (no gaps are stripped).
`strand`	Either "+" or "-". If "-", reverse complement the alignment.

An object of type msa. It will be the same as the original msa, with the following modifications:

If refseq is not NULL, columns with gaps in refseq will be stripped.
If strand is "-", the new msa will be the reverse complement of the original.
After the gap stripping and reverse complementing steps, each sequence is searched for stop codons. If encountered, the stop codon and the rest of the sequence to follow is converted to missing data. The resulting msa has a length equal to the longest remaining sequence (end columns with all missing data are removed).

If the input msa (x) is stored as a pointer, its value will be changed to the return value of the function.

Melissa J. Hubisz

rphast documentation built on May 1, 2019, 9:26 p.m.