@code{(require 'ncbi-dma)}
@ftindex ncbi-dma


@defun ncbi:read-dna-sequence port

Reads the NCBI-format DNA sequence following the word @samp{ORIGIN}
from @var{port}.
@end defun


@defun ncbi:read-file file

Reads the NCBI-format DNA sequence following the word @samp{ORIGIN}
from @var{file}.
@end defun


@defun mrna<-cdna str

Replaces @samp{T} with @samp{U} in @var{str}
@end defun


@defun codons<-cdna cdna

Returns a list of three-letter symbol codons comprising the protein
sequence encoded by @var{cdna} starting with its first occurence of
@samp{atg}.
@end defun


@defun protein<-cdna cdna

Returns a list of three-letter symbols for the protein sequence
encoded by @var{cdna} starting with its first occurence of @samp{atg}.
@end defun


@defun p<-cdna cdna

Returns a string of one-letter amino acid codes for the protein
sequence encoded by @var{cdna} starting with its first occurence of
@samp{atg}.
@end defun


These cDNA count routines provide a means to check the nucleotide
sequence with the @samp{BASE COUNT} line preceding the sequence from
NCBI.


@defun cdna:base-count cdna

Returns a list of counts of @samp{a}, @samp{c}, @samp{g}, and
@samp{t} occurrencing in @var{cdna}.
@end defun


@defun cdna:report-base-count cdna

Prints the counts of @samp{a}, @samp{c}, @samp{g}, and @samp{t}
occurrencing in @var{cdna}.
@end defun

