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Resources

Resources data are stored in an XML file, "Chromosomes.xml". It contains a description of a full haploid set of chromosome of the species of interest at relevant banding resultions.

The file included with the ISCNAnalyser describes human chromosomes. For the analysis of other species, this file may be replaced with the respective chromosome defintions of the species of interest in the same data format. Note that the description of chromosomal bands must be compatible with the description of human chromosomes (e.g. gorilla, chimpanzee). Note that the description of the all acrocentric chromosomes of mice is not compatible and cannot be analysed with this software.

It is a hierarchical description of the following units:

General data
Chromosome
Arm
Landmark (or Region)
Band
SubBand

Programming Language

Microsoft Visual Basic .Net.

Availability

Copyrighted but free software under the GNU Public License.
Binaries and source code can be obtained from the Download section.

General data

General data provide information on the Genus whose chromosomes are describes here, a default drawing order, the maximum height of a chromosome in pixels, the maximum number of a chromosome and the number of chromosomes in an haploid set.

Name	Meaning	Type	Amount
Genus	name of the genus whose chrosomes are described here.	String	1
DrawSequence	a comma separated list of chromosome numbers showing the sequence in which chromosomes are to be drawn by default.	String	1
MAX_CHROMOSOME_HEIGHT	the height of the largest chromosome in pixels when drawn at scale 1. A bigger than the actual value may be given, but that would reduce performance.	Integer	1
MAX_CHROMOSOME_NUMBER	with the exception of the sex chromosomes, chromosomes are numbered with numbers. This field contains the maximum number given to a chromosome.	Integer	1
CHROMOSOMES_PER_HAPLOID_SET	the amount of chromosomes in an haploid set.	Integer	1
Chromosome	description of a chromosome (see below)		0, 1, or many

Chromosome

A chromosome is identified by its number. A default color for drawing in color is provided. A chromosome has 1 or 2 arms.

Name	Meaning	Type	Amount
Number	number of the chrosome described here.	Integer, X, Y	1
DefaultColor	default color when drawing the chromosome (must be a valid color name from the System.Drawing.KnownColor collection).	String	1
Arm	description of a chromosome arm (see below)		1 or 2

Arm

A chromosomal arm belongs to a chromosome and is identified by its full name. The band number of its terminus is denoted at maximum resolution.

Name	Meaning	Type	Amount
Parentt	number of the chrosome this arm belongs to.	Integer, X, Y	1
FullName	the full name of the arm (e.g. "1p").	String	1
Name	name of the arm only (e.g. "p")	"p" or "q"	1
Terminus	band number of the terminus at maximum resolution (e.g. "3633" for p arm of #1)	String	1
Landmark	description of a landmark on the chromosomal arm (see below)		1 or many

Landmark

A landmark describes a larger region on a chromosomal arm.

Name	Meaning	Type	Amount
Parentt	the FullName of the arm the landmark belongs to.	String	1
FullName	the full name of the landmark (e.g. "1p3").	String	1
Number	the number only of the landmark (e.g. "3" for landmark "1p3")	String (Length 1)	1
Band	description of a band belonging to this landmark (see below).		1 or many

Band

A band describes a chromosomal band. Apart from its name and its place in the hierarchical structure, information is provided about the banding resolution satisfied with this band number and data for drawing.

Name	Meaning	Type	Amount
Parentt	the FullName of the landmark the band belongs to.	String	1
FullName	the full name of the band (e.g. "1p36").	String	1
Number	the number only of the band (e.g. "36" for landmark "1p36").	String (Length 2)	1
SatisfiesResolution	the banding resolution satisfied with this band number ("0" if less than 400 bphs).	Integer	1
Height	the height of the band in pixels.	Integer	1
Paint	the style for drawing the band.	PaintStyle	1
SubBand	description of a sub-band belonging to this band (see below).		0 or many

PaintStyle

PaintStyle is an enumeration of styles for drawing a chromosomal band.

Name	Meaning
full	all the area of the band is filled with color.
dark	the area of the band is filled with a hatched pattern of thick lines from upper right to lower left.
light	the area of the band is filled with a hatched pattern of thin lines from upper left to lower right.
transparent	the area of the band remains transparent, only the conturs are drawn.
none	the paint style for the band is not defined.

Subband

At higher resolution, bands may resolve into subbands. The properties are almost the same as with band.

Name	Meaning	Type	Amount
Parentt	the FullName of the band or subband the subband belongs to.	String	1
FullName	the full name of the band (e.g. "1p363").	String	1
Number	the number only of the subband (e.g. "363" for landmark "1p363").	String (Length 3 or more)	1
SatisfiesResolution	the banding resolution satisfied with this subband number ("0" if less than 400 bphs).	Integer	1
Height	the height of the subband in pixels.	Integer	1
Paint	the style for drawing the subband.	PaintStyle	1
SubBand	description of a sub-band belonging to this subband.		0 or many