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

Syntax

Input Arguments

Seq

One of the following: String of codes 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]
   

See Also

aacount | basecount | codoncount | dimercount

© 1984-2012- The MathWorks, Inc.    -   Site Help   -   Patents   -   Trademarks   -   Privacy Policy   -   Preventing Piracy   -   RSS