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Read Protein Sequences in FASTA Format

Source: R/501-readFASTA.R
readFASTA.Rd

Reads protein sequences in FASTA format.

Usage

readFASTA(
  file = system.file("protseq/P00750.fasta", package = "Rcpi"),
  legacy.mode = TRUE,
  seqonly = FALSE
)

Arguments

file

The name of the file which the sequences in fasta format are to be read from. If it does not contain an absolute or relative path, the file name is relative to the current working directory, getwd. The default here is to read the P00750.fasta file which is present in the protseq directory of the Rcpi package.

legacy.mode

If set to TRUE, lines starting with a semicolon ';' are ignored. Default value is TRUE.

seqonly

If set to TRUE, only sequences as returned without attempt to modify them or to get their names and annotations (execution time is divided approximately by a factor 3). Default value is FALSE.

Value

Character vector.

References

Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America, 85: 2444-2448.

See also

See readPDB for reading protein sequences in PDB format.

Examples

P00750 = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))
P00750
#> $`sp|P00750|TPA_HUMAN`
#> [1] "MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARSYQVICRDEKTQMIYQQHQSWLRPVLRSNRVEYCWCNSGRAQCHSVPVKSCSEPRCFNGGTCQQALYFSDFVCQCPEGFAGKCCEIDTRATCYEDQGISYRGTWSTAESGAECTNWNSSALAQKPYSGRRPDAIRLGLGNHNYCRNPDRDSKPWCYVFKAGKYSSEFCSTPACSEGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP"
#>