Bioinformatics Toolbox™

nmercount - Count n-mers in nucleotide or amino acid sequence

Syntax

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

Arguments

Return Values

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]
   

See Also

Bioinformatics Toolbox™ functions: aacount, basecount, codoncount, dimercount

mzxmlread

nt2aa