read.all {seq2R} | R Documentation |
Read nucleic acid sequences from a file in FASTA or GBK format.
read.all(file = system.file(""), seqtype = "DNA")
file |
The name of the file which the sequences in FASTA or GBK format are to be read from. |
seqtype |
The nature of the sequence. Nowadays only |
Fasta is a widely used format in molecular biology. Sequence in FASTA format starts with a single-line description, distinguished by a greater-than ‘>’ symbol, followed by sequence data on the next lines.
'GenBank' format files have the extension GBK, by convention. Files contain fields with different types of information well-labeled. The header of the file has information describing the sequence, such as its type, shape, length and source. The features of the genome sequence follow the header, and include protein translations. The DNA sequence is the last element of the file, which ends with (and must include) a soluble slash. Complete genomes in this format are available at the https://ftp.ncbi.nlm.nih.gov/genbank/.
Sequence |
The returned list has a component |
Locus or accession |
the returned list has a component |
Nora M. Villanueva and Marta Sestelo.
library(seq2R)
data(mtDNAhum)
## Not run:
data<-read.all("file.fasta")
data<-read.all("file.gbk")
## End(Not run)