Protein Sequence Segmentation
Usage
segProt(
x,
aa = c("A", "R", "N", "D", "C", "E", "Q", "G", "H", "I", "L", "K", "M", "F", "P", "S",
"T", "W", "Y", "V"),
k = 7
)Arguments
- x
A character vector, as the input protein sequence.
- aa
A character, the amino acid type. one of
'A','R','N','D','C','E','Q','G','H','I','L','K','M','F','P','S','T','W','Y','V'.- k
A positive integer, specifys the window size (half of the window), default is 7.
Value
A named list, each component contains one of the segmentations (a character string), names of the list components are the positions of the specified amino acid in the sequence.
Examples
x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]
segProt(x, aa = 'R', k = 5)
#> $`6`
#> [1] "MDAMKRGLCCV"
#>
#> $`29`
#> [1] "QEIHARFRRGA"
#>
#> $`31`
#> [1] "IHARFRRGARS"
#>
#> $`32`
#> [1] "HARFRRGARSY"
#>
#> $`35`
#> [1] "FRRGARSYQVI"
#>
#> $`42`
#> [1] "YQVICRDEKTQ"
#>
#> $`58`
#> [1] "HQSWLRPVLRS"
#>
#> $`62`
#> [1] "LRPVLRSNRVE"
#>
#> $`65`
#> [1] "VLRSNRVEYCW"
#>
#> $`75`
#> [1] "WCNSGRAQCHS"
#>
#> $`90`
#> [1] "SCSEPRCFNGG"
#>
#> $`124`
#> [1] "CEIDTRATCYE"
#>
#> $`136`
#> [1] "QGISYRGTWST"
#>
#> $`164`
#> [1] "KPYSGRRPDAI"
#>
#> $`165`
#> [1] "PYSGRRPDAIR"
#>
#> $`170`
#> [1] "RPDAIRLGLGN"
#>
#> $`180`
#> [1] "NHNYCRNPDRD"
#>
#> $`184`
#> [1] "CRNPDRDSKPW"
#>
#> $`224`
#> [1] "NGSAYRGTHSL"
#>
#> $`268`
#> [1] "KHNYCRNPDGD"
#>
#> $`284`
#> [1] "HVLKNRRLTWE"
#>
#> $`285`
#> [1] "VLKNRRLTWEY"
#>
#> $`302`
#> [1] "STCGLRQYSQP"
#>
#> $`310`
#> [1] "SQPQFRIKGGL"
#>
#> $`333`
#> [1] "IFAKHRRSPGE"
#>
#> $`334`
#> [1] "FAKHRRSPGER"
#>
#> $`339`
#> [1] "RSPGERFLCGG"
#>
#> $`362`
#> [1] "HCFQERFPPHH"
#>
#> $`374`
#> [1] "TVILGRTYRVV"
#>
#> $`377`
#> [1] "LGRTYRVVPGE"
#>
#> $`418`
#> [1] "KSDSSRCAQES"
#>
#> $`427`
#> [1] "ESSVVRTVCLP"
#>
#> $`462`
#> [1] "PFYSERLKEAH"
#>
#> $`469`
#> [1] "KEAHVRLYPSS"
#>
#> $`475`
#> [1] "LYPSSRCTSQH"
#>
#> $`484`
#> [1] "QHLLNRTVTDN"
#>
#> $`497`
#> [1] "CAGDTRSGGPQ"
#>
#> $`524`
#> [1] "CLNDGRMTLVG"
#>
#> $`557`
#> [1] "YLDWIRDNMRP"
#>