basecount

Count nucleotides in sequence

Syntax

NTStruct = basecount(SeqNT)

NTStruct = basecount(SeqNT,Name=Value)

Description

NTStruct = basecount(SeqNT) returns the number of each type of base in SeqNT.

NTStruct = basecount(SeqNT,Name=Value) uses additional options specified by one or more name-value arguments.

Examples

Count Nucleotides in Sequence

Count the bases in a DNA sequence and return the results in a structure.

bases = basecount('TAGCTGGCCAAGCGAGCTTG')

bases = struct with fields:
    A: 4
    C: 5
    G: 7
    T: 4

Get the number of adenosine (A) bases.

bases.A

ans = 
4

Create a bar graph comparing the number of each nucleotide.

basecount('TAGCTGGCCAAGCGAGCTTG',Chart="bar")

ans = struct with fields:
    A: 4
    C: 5
    G: 7
    T: 4

Count the bases in a DNA sequence containing ambiguous characters (R, Y, K, M, S, W, B, D, H, V, or N), listing each of them in a separate field.

basecount('ABCDGGCCAAGCGAGCTTG',Ambiguous="individual")

ans = struct with fields:
    A: 4
    C: 5
    G: 6
    T: 2
    R: 0
    Y: 0
    K: 0
    M: 0
    S: 0
    W: 0
    B: 1
    D: 1
    H: 0
    V: 0
    N: 0

Input Arguments

SeqNT — Nucleotide sequence

character vector | string scalar | row vector of integers | structure

Nucleotide sequence, specified as one of the following.

• Character vector or string scalar consisting of the characters A, C, G, T, and U, and ambiguous characters R, Y, K, M, S, W, B, D, H, V, and N.

• Row vector of integers specifying a nucleotide sequence. For information on valid integers, see Mapping Nucleotide Integers to Letter Codes.

• Structure that contains a nucleotide sequence in the Sequence field. The fastaread, fastqread, emblread, getembl, genbankread, and getgenbank functions return structures with a Sequence field.

Example: NTStruct = basecount('CGACTT') counts the number of times of each nucleotide occurs in the sequence.

Data Types: double | char | string | struct

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: NTStruct = basecount("ACGGTC",Ambiguous="individual")

Ambiguous — Method for counting ambiguous nucleotide characters

"ignore" (default) | "bundle" | "prorate" | "individual" | "warn"

Method for counting ambiguous nucleotide characters (R, Y, K, M, S, W, B, D, H, V, and N), specified as one of the following.

• "ignore" — basecount skips ambiguous characters.

• "bundle" — basecount counts ambiguous characters and reports the total count in the Ambiguous field.

• "prorate" — basecount counts ambiguous characters and distributes the total number evenly between all possible unambiguous nucleotide fields. For example, the count for the character R is distributed evenly between the A and G fields.

• "individual" — basecount counts ambiguous characters and reports them in individual fields.

• "warn" — basecount skips ambiguous characters and displays a warning.

Example: NTStruct = basecount("CGRTTMSA",Ambiguous="bundle") reports the total number of ambiguous characters in the Ambiguous field of NTStruct.

Data Types: char | string

Gaps — Flag to count or ignore gaps

false (default) | true

Flag to count or ignore gaps, specified as true or false. Gaps are indicated by a hyphen (-).

If you set this option to true, then basecount counts the gaps and reports the total count in the Gaps field.

Data Types: logical

Chart — Type of chart

"pie" | "bar"

Type of chart to display the proportions of nucleotides, specified as "pie" or "bar".

Data Types: char | string

Output Arguments

NTStruct — Nucleotide counts

structure

Nucleotide counts, returned as a structure containing the fields A, C, G, and T. Uracil nucleotides (U) are added to the T field. Additional fields can be present, depending on the value of Ambiguous and Gaps.

Version History

Introduced before R2006a