nmercount

Count n-mers in nucleotide or amino acid sequence

Syntax

Nmer = nmercount(Seq, Length)
Nmer = nmercount(Seq, Length, C)


Input Arguments

Seq

One of the following: Character vector or string specifying a nucleotide sequence or amino acid sequence. For valid letter codes, see the table Mapping Nucleotide Letter Codes to Integers or the table Mapping Amino Acid Letter Codes to Integers. MATLAB® structure containing a Sequence field that contains a nucleotide sequence or an amino acid sequence, such as returned by fastaread, fastqread, emblread, getembl, genbankread, getgenbank, getgenpept, genpeptread, getpdb, or pdbread.

Length

Integer specifying the length of n-mer to count.

Output Arguments

Nmer	Cell array containing the n-mer counts in Seq.

Description

Nmer = nmercount(Seq, Length) counts the n-mers or patterns of a specific length in Seq, a nucleotide sequence or amino acid sequence, and returns the n-mer counts in a cell array.

Nmer = nmercount(Seq, Length, C) returns only the n-mers with cardinality of at least C.

Examples

1. Use the getgenpept function to retrieve the amino acid sequence for the human insulin receptor.

   S = getgenpept('AAA59174','SequenceOnly',true);

2. Count the number of four-mers in the amino acid sequence and display the first 20 rows in the cell array.

   nmers = nmercount(S,4);
   nmers(1:20,:)
   
   ans = 
       'APES'    [2]
       'DFRD'    [2]
       'ESLK'    [2]
       'FRDL'    [2]
       'GNYS'    [2]
       'LKEL'    [2]
       'SHCQ'    [2]
       'SLKD'    [2]
       'SVRI'    [2]
       'TDYL'    [2]
       'TSLA'    [2]
       'TVIN'    [2]
       'VING'    [2]
       'VPLD'    [2]
       'YALV'    [2]
       'AAAA'    [1]
       'AAAP'    [1]
       'AAEI'    [1]
       'AAEL'    [1]
       'AAFP'    [1]