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cytobandread

Read cytogenetic banding information

Syntax

CytoStruct = cytobandread(File)

Input Arguments

FileCharacter vector specifying a file containing cytogenetic G-banding data, such as an NCBI ideogram text file or a UCSC Genome Browser cytoband text file.

Output Arguments

CytoStructStructure containing cytogenetic G-banding data in the following fields:
  • ChromLabels

  • BandStartBPs

  • BandEndBPs

  • BandLabels

  • GieStains

Description

CytoStruct = cytobandread(File) reads File, which is a character vector specifying a file containing cytogenetic G-banding data, and returns CytoStruct, which is a structure containing the following fields.

FieldDescription
ChromLabelsCell array containing the chromosome label (number or letter) on which each band is located.
BandStartBPsColumn vector containing the number of the base pair at the start of each band.
BandEndBPsColumn vector containing the number of the base pair at the end of each band.
BandLabelsCell array containing the FISH label of each band, for example, p32.3.
GieStainsCell array containing the Giemsa staining result for each band. Possible stain results depend on the species. For example, for Homo sapiens, the possibilities are:
  • gneg

  • gpos25

  • gpos50

  • gpos75

  • gpos100

  • acen

  • stalk

  • gvar

Tip

You can download files containing cytogenetic G-banding data from the NCBI or UCSC Genome Browser ftp site. For example, you can download the cytogenetic banding data for Homo sapiens from:

or

Examples

collapse all

Read the cytogenetic banding information for Homo sapiens into a structure.

bands = cytobandread('hs_cytoBand.txt')
bands = 

  struct with fields:

     ChromLabels: {862x1 cell}
    BandStartBPs: [862x1 int32]
      BandEndBPs: [862x1 int32]
      BandLabels: {862x1 cell}
       GieStains: {862x1 cell}

Plot the entire chromosome ideogram.

chromosomeplot(bands)
title('Human Karyogram')

Introduced in R2007b

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