R: Calculates the average bulkiness of amino acid sequences

bulk {alakazam} | R Documentation

## Calculates the average bulkiness of amino acid sequences

### Description

`bulk` calculates the average bulkiness score of amino acid sequences. Non-informative positions are excluded, where non-informative is defined as any character in `c("X", "-", ".", "*")`.

### Usage

    bulk(seq, bulkiness = NULL)

### Arguments

`seq` | vector of strings containing amino acid sequences.
`bulkiness` | named numerical vector defining bulkiness scores for each amino acid, where names are single-letter amino acid character codes. If `NULL`, then the Zimmerman et al, 1968 scale is used.

### Value

A vector of bulkiness scores for the sequence(s).

### References

1. Zimmerman JM, Eliezer N, Simha R. The characterization of amino acid sequences in proteins by statistical methods. J Theor Biol 21, 170-201 (1968).

### See Also

For additional size related indices see aaindex.

### Examples

    # Default bulkiness scale
    seq <- c("CARDRSTPWRRGIASTTVRTSW", "XXTQMYVRT")
    bulk(seq)

    # Use the Grantham, 1974 side chain volumn scores from the seqinr package
    library(seqinr)
    data(aaindex)
    x <- aaindex[["GRAR740103"]]$I
    # Rename the score vector to use single-letter codes
    names(x) <- translateStrings(names(x), ABBREV_AA)
    # Calculate average volume
    bulk(seq, bulkiness=x)

[Package alakazam version 0.3.0 Index]