[Bioperl-l] Where could I find FISH Map information in mapview data or somewhere else?

[Heikki Lehvaslaiho]

Dear Snag Chul Choi,

There is nothing bioperl that would draw the chromosomes for you, but I
can show how to get the data. It involves taking the details from the
human Ensembl (http://www.ensembl.org/) database. I'll first show how
you can manually browse the information and then easily download the
data.

1. Log into the public ensembl database using a mysql client.

   % mysql -uanonymous -h kaka.sanger.ac.uk

2. 'show databases;' lists the them all, but the latest human
   core database can currently be activated by:

   mysql> use homo_sapiens_core_14_31;

3. The data you need is in table 'karyotype'

   mysql> describe karyotype;
+---------------+------------------+------+-----+---------+-------+
| Field         | Type             | Null | Key | Default | Extra |
+---------------+------------------+------+-----+---------+-------+
| chromosome_id | int(10) unsigned |      | PRI | 0       |       |
| chr_start     | int(10)          |      |     | 0       |       |
| chr_end       | int(10)          |      |     | 0       |       |
| band          | varchar(40)      |      | PRI |         |       |
| stain         | varchar(40)      |      |     |         |       |
+---------------+------------------+------+-----+---------+-------+
5 rows in set (0.01 sec)

    and looks like this:

    mysql> select * from karyotype limit 5;
+---------------+-----------+----------+--------+--------+
| chromosome_id | chr_start | chr_end  | band   | stain  |
+---------------+-----------+----------+--------+--------+
|             1 |         0 |  2200000 | p36.33 | gneg   |
|             1 |   2200000 |  5100000 | p36.32 | gpos25 |
|             1 |   5100000 |  6900000 | p36.31 | gneg   |
|             1 |   6900000 |  8900000 | p36.23 | gpos25 |
|             1 |   8900000 | 12200000 | p36.22 | gneg   |
+---------------+-----------+----------+--------+--------+
5 rows in set (0.03 sec)

5. Since you are now connected to a remote host where you have not write
privileges, you can not save data. Log out.

   mysql> exit

6. Run this from the command line:

  % mysql -uanonymous -h kaka.sanger.ac.uk -e \
    'select * from karyotype' homo_sapiens_core_14_31 \
    > karyotype.tab


If you do not have a suitable mysql client and can not get the data, let
me know and I'll mail the karyotype.tab file to you.

Yours,
	-Heikki


On Tue, 2003-07-01 at 08:01, Sang Chul Choi wrote:
> Dear bioperl GURU:
> 
> NCBI's mapview data is so useful: it has contig assembly data, gene data, etc.
> There is also FISH map information in "cyto_clone.md" file.

> However, I could not find out how ideogram could be painted. I wish I could have 
> like these data:
> 
>             chromosome_start            chromosome_end
> 6p22.3  2000000                             3000000
> 6p22.2  3000001                             4000000
> 
> I would like to draw colorful chromosomes, how could I do that?
> 
> Thank you in advance.
> 
> Sincerely yours,
> 
> Sang Chul Choi
> 
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> Bioperl-l at portal.open-bio.org
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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