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4.14 NCBI-DNA

(require 'ncbi-dma)

— Function: ncbi:read-dna-sequence port

Reads the NCBI-format DNA sequence following the word ‘ORIGIN’ from port.

— Function: ncbi:read-file file

Reads the NCBI-format DNA sequence following the word ‘ORIGIN’ from file.

— Function: mrna<-cdna str

Replaces ‘T’ with ‘U’ in str

— Function: codons<-cdna cdna

Returns a list of three-letter symbol codons comprising the protein sequence encoded by cdna starting with its first occurence of ‘atg’.

— Function: protein<-cdna cdna

Returns a list of three-letter symbols for the protein sequence encoded by cdna starting with its first occurence of ‘atg’.

— Function: p<-cdna cdna

Returns a string of one-letter amino acid codes for the protein sequence encoded by cdna starting with its first occurence of ‘atg’.

These cDNA count routines provide a means to check the nucleotide sequence with the ‘BASE COUNT’ line preceding the sequence from NCBI.

— Function: cdna:base-count cdna

Returns a list of counts of ‘a’, ‘c’, ‘g’, and ‘t’ occurrencing in cdna.

— Function: cdna:report-base-count cdna

Prints the counts of ‘a’, ‘c’, ‘g’, and ‘t’ occurrencing in cdna.