iPE::Util::DNATools(3)

NAME
iPE::Util::DNATools - A set of functions to analyze DNA sequences.

DESCRIPTION
A set of functions which do various things to extract information about or perform transformations on DNA sequences.

FUNCTIONS

reverseComplement (stringRef)
    Return the reverse complement of a DNA sequence including upper- and lower-case ambiguity codes. Only references are passed in and out to prevent overflow of memory for large sequences.

    Note that S's and W's remain the same since they represent complements.

rcCoords (high, low, length)
    Returns an array containing the low and high coordinates of a region as it would be on the reverse complement sequence on a 0-based index.

getOpposingFrame(start, end, frame)
    Infers the frame at the other end of the feature given its coordinates and opposing frame. Specifically, given the number of overhanging bases on one end of the (CDS) feature, get the number of overhanging bases on the other end of the feature.

gcContent
    Return the GC% of a sequence which may include ambiguity codes.

levels (sequence)
    Return a hash reference to the levels of each of the canonical DNA codes, A, C, G, and T. The sequence can include ambiguity codes and the levels are appropriately measured.

fast_uc (stringref, length)
    This function is a fast, memory efficient version of the uc routine.

SEE ALSO
iPE

AUTHOR
Bob Zimmermann (rpz@cse.wustl.edu)