getFfnFaa: Extract CDS gene (DNA) and protein (AA) sequences
In iferres/phylen: Search Core Genes Using HMMs, Compute Multiple Alignment, Concatenate And Compute Phylogeny
Description
Usage
Arguments
Value
Author(s)
Description
Extract CDS gene (DNA) and protein (AA) sequences from both a
gff3 table and the fasta sequence.
Usage
1
getFfnFaa(fnas, contig, strand, from, to, id, product)
Arguments
fnas
A list of SeqFastadna genome sequences.
contig
character. The name of the contig.
strand
character. Either "+" or "-".
from
numeric. The coordinate "from".
to
numeric. The coordinate "to".
id
character. The ID of the CDS.
product
character. The gene product.
Value
A list with two entries. The first is the CDS's DNA sequence,
and the last is the protein sequence. Object classes are SeqFastadna
and SeqFastaAA, respectively.
Author(s)
Ignacio Ferres
iferres/phylen documentation built on May 24, 2019, 2:04 a.m.
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Description Usage Arguments Value Author(s)
Description
Extract CDS gene (DNA) and protein (AA) sequences from both a gff3 table and the fasta sequence.
Usage
1 | getFfnFaa(fnas, contig, strand, from, to, id, product)
|
Arguments
fnas |
A |
contig |
|
strand |
|
from |
|
to |
|
id |
|
product |
|
Value
A list with two entries. The first is the CDS's DNA sequence,
and the last is the protein sequence. Object classes are SeqFastadna
and SeqFastaAA, respectively.
Author(s)
Ignacio Ferres
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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