Doubt about cytobands

[Amruta Nambiar]

Hi Team,

I am Amruta B Nambiar a Bioinformatics enthusiast from India.

From the following link http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ I have downloaded the cytoBand.txt.gz and cytoBandIdeo.txt.gz   files.The cytoBandIdeo.txt file contains all data cytoBand.txt  and also some additional data as shown below

chr11_gl000202_random         0             40103                     gneg

chr21_gl000210_random         0             27682                     gneg

chrM        0             16571                     gneg

chrUn_gl000211       0             166566                    gneg

chrUn_gl000212       0             186858                    gneg

chrUn_gl000213       0             164239                    gneg

chrUn_gl000214       0             137718                    gneg

 

What is the difference between cytoBand.txt   and cytoBandIdeo.txt file?

What does different stain values gneg,gpos25,gpos50 , gpos75,gpos100,acen,stalk,gvar etc indicate. Which region in chromsomes they indicate?

Thanks and Regards,

Amruta B Nambiar

[robert kuhn]

Hello, Amruta,

There should be little difference between the cytoBand.txt and the
cytoBandIdeo.txt
files. Each of our data tracks is supported by one file (table in the
database) with
coordinates for mapping. The *Ideo* file underlies the graphic display
of the
cytoband data in the small ideogram graphic above the main Browser display.

The cytoBandIdeo file/table has been modified from the cytoBand
file/table for
purposes of the display in the ideogram. The cytoBand table/file
underlies the
data track in the main Browser graphic and should be the file used for most
purposes.

The items in the last column refer to the coloring you see in the both the
Browser graphic and in the ideogram above. The first 5 in the list below
reflect the level of color obtained via Giemsa staining; "acen" is
centromeric;
"stalk" refers to the short arm of acrocentric chromosomes
chr13,14,15,21,22;
"gvar" bands tend to be heterochomatin, either pericentric or telomeric.
The
best way to see for your self is to look at the regions in the Genome
Browser.

<pre>
+----------+
| gieStain |
+----------+
| gneg |
| gpos25 |
| gpos50 |
| gpos75 |
| gpos100 |
| acen |
| gvar |
| stalk |
+----------+
</pre>

best wishes and thanks for being a Genome Browser user.

--b0b kuhn
ucsc genome bioinformatics group

On 7/6/2014 10:31 PM, Amruta Nambiar wrote:
>
> Hi Team,
>
>
> I am Amruta B Nambiar a Bioinformatics enthusiast from India.
>
> From the following link

> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/I have

> downloaded the cytoBand.txt.gz and cytoBandIdeo.txt.gz files.The

> cytoBandIdeo.txt file contains all data cytoBand.txtand also some

> additional data as shown below
>
> chr11_gl000202_random040103gneg
>
> chr21_gl000210_random027682gneg
>
> chrM016571gneg
>
> chrUn_gl0002110166566gneg
>
> chrUn_gl0002120186858gneg
>
> chrUn_gl0002130164239gneg
>
> chrUn_gl0002140137718gneg
>

> What is the difference between cytoBand.txtand cytoBandIdeo.txt file?

>
> What does different stain values gneg,gpos25,gpos50

> ,gpos75,gpos100,acen,stalk,gvar etc indicate. Which region in

> chromsomes they indicate?
>
>
> Thanks and Regards,
>
> Amruta B Nambiar
>
>

> --
>