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.