cytobandread

Read cytogenetic banding information

Syntax

CytoStruct = cytobandread(File)


Input Arguments

File	Character vector or string 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

CytoStruct

Structure 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 or string specifying a file containing cytogenetic G-banding data, and returns CytoStruct, which is a structure containing the following fields.

Field	Description
ChromLabels	Cell array containing the chromosome label (number or letter) on which each band is located.
BandStartBPs	Column vector containing the number of the base pair at the start of each band.
BandEndBPs	Column vector containing the number of the base pair at the end of each band.
BandLabels	Cell array containing the FISH label of each band, for example, p32.3.
GieStains	Cell 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 web site. For example, you can download the cytogenetic banding data (cytoBandIdeo.txt.gz) for Homo sapiens from:

https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

Examples

Read cytogenetic banding information from a file

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')

Version History

Introduced in R2007b