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:
|
Description
CytoStruct = cytobandread(File)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:
|
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:
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')