GAL file format

December 9th, 2011

GenePix Array List (GAL) files are text files with specific information about the location, size, and name of each DNA spot on a microarray. They are therefor of vital importance for the analysis of scanned microarray images.

The format defines a specific header before the list of data columns follows:

Example:


ATF	1			

9	5			

Type=GenePix ArrayList V1.0				

BlockCount=1				

BlockType=0				

"Block1=10000, 38780, 150, 20, 200, 18, 200"				

Supplier=BioRobotics				

ArrayerSoftwareName=TAS Application Suite (MicroGrid II)				

ArrayerSoftwareVersion=2.7.1.18					

ScanResolution=10	

Block	Column	Row	ID	Name

1	1	1	RP11-163J21	Clone 1

1	1	2	RP11-163J21	Clone 2

Explanantions:

ATF -> File conforms to Axon Text File

1 -> Version number of ATF

9 -> Number of header lines before the "Block, Column, Row, ..." line

5 -> Number of data columns (Block, Column, Row, Name, ID)

Type=GenePix ArrayList V1.0 -> Type of file, same for all GAL files

Block Count=1 -> Number of blocks described in the file

Block Type=0 -> Type of block, 0 = rectangular

BlockX=A, B, C, D, E, F, G -> The position and dimensions of each block.

A -> xOrigin

B -> yOrigin

C -> Feature diameter

D -> xFeatures

E -> xSpacing

F -> yFeatures

G -> ySpacing

ScanResolution - Optional parameter to scale the position on higher-resolution images

Block arrangement

1	2	3	4

5	6	7	8

9	10	11	12

13	14	15	16

The data columns are:

  • Block
  • Column
  • Row
  • Name
  • ID

Further reading and sources:

Telomeric and Centromeric regions

September 22nd, 2011

Telomeres form caps on the ends of chromosomes that prevent fusion of chromosomal ends and provide genomic stability.

During gametogenesis, reprogramming of the germ cells leads to elongation of telomeres up to their species-specific maximum.

In normal somatic cells, telomeres are progressively shortened with every cell division. This shortening in normal human cells limits the number of cell divisions. For human cells to proliferate beyond the senescence checkpoint, they need to stabilize telomere length. This is accomplished mainly by reactivation of the telomerase enzyme. Telomerase expression is under the control of many factors. Expression of telomerase can lead to cell immortalization and is activated during tumorigenesis, i.e. cancer.

Male Xq-telomeres are 1100 bp shorter than female Xq-telomeres.

The telomeric repeat found on all human chromosomes is "TTAGGG".

The centromeres and telomeres of the human chromosomes are not defined as region attributes in the Ensembl perl API explicitely, so for checking these regions, one option is to pull them out of the UCSC table browser (use the "Mapping and Sequencing tracks" group and the "Gap" table) and define them manually. You can e.g. create an array of hashes with the regions and use them in your script:

Code

#read data (listed below) from a file...
my @data = split("\s");
my %telomere = (
      'chrom' => $data[0],
      'start' => $data[1],
      'end'   => $data[2],
   );
push(@telomeres, \%telomere);

The list of centromere regions (transformed from the 0-based UCSC system to the 1-based coordinated system) for GRCh37 is:

Code

1       121535435       124535434
2       92326172       95326171
3       90504855       93504854
4       49660118       52660117
5       46405642       49405641
6       58830167       61830166
7       58054332       61054331
8       43838888       46838887
9       47367680       50367679
10      39254936       42254935
11      51644206       54644205
12      34856695       37856694
13      16000001       19000000
14      16000001       19000000
15      17000001       20000000
16      35335802       38335801
17      22263007       25263006
18      15460899       18460898
19      24681783       27681782
20      26369570       29369569
21      11288130       14288129
22      13000001       16000000
X       58632013       61632012
Y       10104554       13104553

The list of telomere regions for GRCh37 is (1-based):

Code

1       1               10000
1       249240622       249250621
2       1               10000
2       243189374       243199373
3       1               10000
3       198012431       198022430
4       1               10000
4       191144277       191154276
5       1               10000
5       180905261       180915260
6       1               10000
6       171105068       171115067
7       1               10000
7       159128664       159138663
8       1               10000
8       146354023       146364022
9       1               10000
9       141203432       141213431
10      135524748       135534747
10      1               10000
11      134996517       135006516
11      1               10000
12      1               10000
12      133841896       133851895
13      1               10000
13      115159879       115169878
14      1               10000
14      107339541       107349540
15      1               10000
15      102521393       102531392
16      1               10000
16      90344754        90354753
18      1               10000
18      78067249        78077248
19      1               10000
19      59118984        59128983
20      1               10000
20      63015521        63025520
21      1               10000
21      48119896        48129895
22      1               10000
22      51294567        51304566
X       1               10000
X       155260561       155270560
Y       1               10000
Y       59363567        59373566

Telomeres of chromosome 17 have not been defined for assembly GRCh37. They are short, but do exists nonetheless. An assembly patch will address this.

Sources:

Cytogenetic Nomenclature

September 6th, 2011

The karyotype (number and set-up of the chromosomes) of a person or any changes in specific regions on human chromosomes are described with a system of numbers and symbols, defined by a group of cytogentic experts as the International System for Human Cytogenetic Nomenclature (ISCN). It was initiated 1960 by a committee after the suggestion of Charles E. Ford resulting in the "Proposed Standard System of Nomenclature of Human Mitotic Chromosomes". The system is based on the ideogram definitions of visual bands (described eg. in Francke et al. 1981), and was last revised 2005 and 2009.

The visual bands are created by staining techniques and describe regions of similarity in respect to functionality and base compositions (GC content); their lengths are 5-10 MB.

Example ideogram of chromosome 1
Example ideograms: Human chromosome 1 in different resolutions, from WashU

Numbers used:

The regions are numbered from the centromer outwards in both directions towards the telomeres on the shorter p arm and the longer q arm. The numbers cannot be read in the normal decimal numeric system e.g. 21, but rather 2-1 (region 2 band 1). Counting starts at the centromer as region 1 (or 1-0), to 11 (1-1) to 21 (2-1) to 22 (2-2) etc. Subbands are added in a similar way, eg. 21.1 to 21.2, if the bands are small or only appear at a higher resolution.

There are different levels of resolution that can be used as bands, e.g. 1q32 in the 400-bands resolution can be split up into 1q32.1, 1q32.2, 1q32.3 in the 550-bands resolution (see Figure above as an example for chr 1).

Here is a list of chromosome, band (arm, region, band, subband), genomic start and end position, from the Ensembl database for assembly GRCh37:

Code

1  p11.1  121500001  125000000  acen
1  p11.2  120600001  121500000  gneg
1  p12  117800001  120600000  gpos50
1  p13.1  116100001  117800000  gneg
1  p13.2  111800001  116100000  gpos50
1  p13.3  107200001  111800000  gneg
1  p21.1  102200001  107200000  gpos100
1  p21.2  99700001  102200000  gneg
1  p21.3  94700001  99700000  gpos75
1  p22.1  92000001  94700000  gneg
1  p22.2  88400001  92000000  gpos75
1  p22.3  84900001  88400000  gneg
1  p31.1  69700001  84900000  gpos100
1  p31.2  68900001  69700000  gneg
1  p31.3  61300001  68900000  gpos50
1  p32.1  59000001  61300000  gneg
1  p32.2  56100001  59000000  gpos50
1  p32.3  50700001  56100000  gneg
1  p33  46800001  50700000  gpos75
1  p34.1  44100001  46800000  gneg
1  p34.2  40100001  44100000  gpos25
1  p34.3  34600001  40100000  gneg
1  p35.1  32400001  34600000  gpos25
1  p35.2  30200001  32400000  gneg
1  p35.3  28000001  30200000  gpos25
1  p36.11  23900001  28000000  gneg
1  p36.12  20400001  23900000  gpos25
1  p36.13  16200001  20400000  gneg
1  p36.21  12700001  16200000  gpos50
1  p36.22  9200001  12700000  gneg
1  p36.23  7200001  9200000  gpos25
1  p36.31  5400001  7200000  gneg
1  p36.32  2300001  5400000  gpos25
1  p36.33  1  2300000  gneg
1  q11  125000001  128900000  acen
1  q12  128900001  142600000  gvar
1  q21.1  142600001  147000000  gneg
1  q21.2  147000001  150300000  gpos50
1  q21.3  150300001  155000000  gneg
1  q22  155000001  156500000  gpos50
1  q23.1  156500001  159100000  gneg
1  q23.2  159100001  160500000  gpos50
1  q23.3  160500001  165500000  gneg
1  q24.1  165500001  167200000  gpos50
1  q24.2  167200001  170900000  gneg
1  q24.3  170900001  172900000  gpos75
1  q25.1  172900001  176000000  gneg
1  q25.2  176000001  180300000  gpos50
1  q25.3  180300001  185800000  gneg
1  q31.1  185800001  190800000  gpos100
1  q31.2  190800001  193800000  gneg
1  q31.3  193800001  198700000  gpos100
1  q32.1  198700001  207200000  gneg
1  q32.2  207200001  211500000  gpos25
1  q32.3  211500001  214500000  gneg
1  q41  214500001  224100000  gpos100
1  q42.11  224100001  224600000  gneg
1  q42.12  224600001  227000000  gpos25
1  q42.13  227000001  230700000  gneg
1  q42.2  230700001  234700000  gpos50
1  q42.3  234700001  236600000  gneg
1  q43  236600001  243700000  gpos75
1  q44  243700001  249250621  gneg
2  p11.1  90500001  93300000  acen
2  p11.2  83300001  90500000  gneg
2  p12  75000001  83300000  gpos100
2  p13.1  73500001  75000000  gneg
2  p13.2  71500001  73500000  gpos50
2  p13.3  68600001  71500000  gneg
2  p14  64100001  68600000  gpos50
2  p15  61300001  64100000  gneg
2  p16.1  55000001  61300000  gpos100
2  p16.2  52900001  55000000  gneg
2  p16.3  47800001  52900000  gpos100
2  p21  41800001  47800000  gneg
2  p22.1  38600001  41800000  gpos50
2  p22.2  36600001  38600000  gneg
2  p22.3  32100001  36600000  gpos75
2  p23.1  30000001  32100000  gneg
2  p23.2  27900001  30000000  gpos25
2  p23.3  24000001  27900000  gneg
2  p24.1  19200001  24000000  gpos75
2  p24.2  16700001  19200000  gneg
2  p24.3  12200001  16700000  gpos75
2  p25.1  7100001  12200000  gneg
2  p25.2  4400001  7100000  gpos50
2  p25.3  1  4400000  gneg
2  q11.1  93300001  96800000  acen
2  q11.2  96800001  102700000  gneg
2  q12.1  102700001  106000000  gpos50
2  q12.2  106000001  107500000  gneg
2  q12.3  107500001  110200000  gpos25
2  q13  110200001  114400000  gneg
2  q14.1  114400001  118800000  gpos50
2  q14.2  118800001  122400000  gneg
2  q14.3  122400001  129900000  gpos50
2  q21.1  129900001  132500000  gneg
2  q21.2  132500001  135100000  gpos25
2  q21.3  135100001  136800000  gneg
2  q22.1  136800001  142200000  gpos100
2  q22.2  142200001  144100000  gneg
2  q22.3  144100001  148700000  gpos100
2  q23.1  148700001  149900000  gneg
2  q23.2  149900001  150500000  gpos25
2  q23.3  150500001  154900000  gneg
2  q24.1  154900001  159800000  gpos75
2  q24.2  159800001  163700000  gneg
2  q24.3  163700001  169700000  gpos75
2  q31.1  169700001  178000000  gneg
2  q31.2  178000001  180600000  gpos50
2  q31.3  180600001  183000000  gneg
2  q32.1  183000001  189400000  gpos75
2  q32.2  189400001  191900000  gneg
2  q32.3  191900001  197400000  gpos75
2  q33.1  197400001  203300000  gneg
2  q33.2  203300001  204900000  gpos50
2  q33.3  204900001  209000000  gneg
2  q34  209000001  215300000  gpos100
2  q35  215300001  221500000  gneg
2  q36.1  221500001  225200000  gpos75
2  q36.2  225200001  226100000  gneg
2  q36.3  226100001  231000000  gpos100
2  q37.1  231000001  235600000  gneg
2  q37.2  235600001  237300000  gpos50
2  q37.3  237300001  243199373  gneg
3  p11.1  87900001  91000000  acen
3  p11.2  87200001  87900000  gneg
3  p12.1  83500001  87200000  gpos75
3  p12.2  79800001  83500000  gneg
3  p12.3  74200001  79800000  gpos75
3  p13  69800001  74200000  gneg
3  p14.1  63700001  69800000  gpos50
3  p14.2  58600001  63700000  gneg
3  p14.3  54400001  58600000  gpos50
3  p21.1  52300001  54400000  gneg
3  p21.2  50600001  52300000  gpos25
3  p21.31  44200001  50600000  gneg
3  p21.32  44100001  44200000  gpos50
3  p21.33  43700001  44100000  gneg
3  p22.1  39400001  43700000  gpos75
3  p22.2  36500001  39400000  gneg
3  p22.3  32100001  36500000  gpos50
3  p23  30900001  32100000  gneg
3  p24.1  26400001  30900000  gpos75
3  p24.2  23900001  26400000  gneg
3  p24.3  16400001  23900000  gpos100
3  p25.1  13300001  16400000  gneg
3  p25.2  11800001  13300000  gpos25
3  p25.3  8700001  11800000  gneg
3  p26.1  4000001  8700000  gpos50
3  p26.2  2800001  4000000  gneg
3  p26.3  1  2800000  gpos50
3  q11.1  91000001  93900000  acen
3  q11.2  93900001  98300000  gvar
3  q12.1  98300001  100000000  gneg
3  q12.2  100000001  100900000  gpos25
3  q12.3  100900001  102800000  gneg
3  q13.11  102800001  106200000  gpos75
3  q13.12  106200001  107900000  gneg
3  q13.13  107900001  111300000  gpos50
3  q13.2  111300001  113500000  gneg
3  q13.31  113500001  117300000  gpos75
3  q13.32  117300001  119000000  gneg
3  q13.33  119000001  121900000  gpos75
3  q21.1  121900001  123800000  gneg
3  q21.2  123800001  125800000  gpos25
3  q21.3  125800001  129200000  gneg
3  q22.1  129200001  133700000  gpos25
3  q22.2  133700001  135700000  gneg
3  q22.3  135700001  138700000  gpos25
3  q23  138700001  142800000  gneg
3  q24  142800001  148900000  gpos100
3  q25.1  148900001  152100000  gneg
3  q25.2  152100001  155000000  gpos50
3  q25.31  155000001  157000000  gneg
3  q25.32  157000001  159000000  gpos50
3  q25.33  159000001  160700000  gneg
3  q26.1  160700001  167600000  gpos100
3  q26.2  167600001  170900000  gneg
3  q26.31  170900001  175700000  gpos75
3  q26.32  175700001  179000000  gneg
3  q26.33  179000001  182700000  gpos75
3  q27.1  182700001  184500000  gneg
3  q27.2  184500001  186000000  gpos25
3  q27.3  186000001  187900000  gneg
3  q28  187900001  192300000  gpos75
3  q29  192300001  198022430  gneg
4  p11  48200001  50400000  acen
4  p12  44600001  48200000  gneg
4  p13  41200001  44600000  gpos50
4  p14  35800001  41200000  gneg
4  p15.1  27700001  35800000  gpos100
4  p15.2  21300001  27700000  gneg
4  p15.31  17800001  21300000  gpos75
4  p15.32  15200001  17800000  gneg
4  p15.33  11300001  15200000  gpos50
4  p16.1  6000001  11300000  gneg
4  p16.2  4500001  6000000  gpos25
4  p16.3  1  4500000  gneg
4  q11  50400001  52700000  acen
4  q12  52700001  59500000  gneg
4  q13.1  59500001  66600000  gpos100
4  q13.2  66600001  70500000  gneg
4  q13.3  70500001  76300000  gpos75
4  q21.1  76300001  78900000  gneg
4  q21.21  78900001  82400000  gpos50
4  q21.22  82400001  84100000  gneg
4  q21.23  84100001  86900000  gpos25
4  q21.3  86900001  88000000  gneg
4  q22.1  88000001  93700000  gpos75
4  q22.2  93700001  95100000  gneg
4  q22.3  95100001  98800000  gpos75
4  q23  98800001  101100000  gneg
4  q24  101100001  107700000  gpos50
4  q25  107700001  114100000  gneg
4  q26  114100001  120800000  gpos75
4  q27  120800001  123800000  gneg
4  q28.1  123800001  128800000  gpos50
4  q28.2  128800001  131100000  gneg
4  q28.3  131100001  139500000  gpos100
4  q31.1  139500001  141500000  gneg
4  q31.21  141500001  146800000  gpos25
4  q31.22  146800001  148500000  gneg
4  q31.23  148500001  151100000  gpos25
4  q31.3  151100001  155600000  gneg
4  q32.1  155600001  161800000  gpos100
4  q32.2  161800001  164500000  gneg
4  q32.3  164500001  170100000  gpos100
4  q33  170100001  171900000  gneg
4  q34.1  171900001  176300000  gpos75
4  q34.2  176300001  177500000  gneg
4  q34.3  177500001  183200000  gpos100
4  q35.1  183200001  187100000  gneg
4  q35.2  187100001  191154276  gpos25
5  p11  46100001  48400000  acen
5  p12  42500001  46100000  gpos50
5  p13.1  38400001  42500000  gneg
5  p13.2  33800001  38400000  gpos25
5  p13.3  28900001  33800000  gneg
5  p14.1  24600001  28900000  gpos100
5  p14.2  23300001  24600000  gneg
5  p14.3  18400001  23300000  gpos100
5  p15.1  15000001  18400000  gneg
5  p15.2  9800001  15000000  gpos50
5  p15.31  6300001  9800000  gneg
5  p15.32  4500001  6300000  gpos25
5  p15.33  1  4500000  gneg
5  q11.1  48400001  50700000  acen
5  q11.2  50700001  58900000  gneg
5  q12.1  58900001  62900000  gpos75
5  q12.2  62900001  63200000  gneg
5  q12.3  63200001  66700000  gpos75
5  q13.1  66700001  68400000  gneg
5  q13.2  68400001  73300000  gpos50
5  q13.3  73300001  76900000  gneg
5  q14.1  76900001  81400000  gpos50
5  q14.2  81400001  82800000  gneg
5  q14.3  82800001  92300000  gpos100
5  q15  92300001  98200000  gneg
5  q21.1  98200001  102800000  gpos100
5  q21.2  102800001  104500000  gneg
5  q21.3  104500001  109600000  gpos100
5  q22.1  109600001  111500000  gneg
5  q22.2  111500001  113100000  gpos50
5  q22.3  113100001  115200000  gneg
5  q23.1  115200001  121400000  gpos100
5  q23.2  121400001  127300000  gneg
5  q23.3  127300001  130600000  gpos100
5  q31.1  130600001  136200000  gneg
5  q31.2  136200001  139500000  gpos25
5  q31.3  139500001  144500000  gneg
5  q32  144500001  149800000  gpos75
5  q33.1  149800001  152700000  gneg
5  q33.2  152700001  155700000  gpos50
5  q33.3  155700001  159900000  gneg
5  q34  159900001  168500000  gpos100
5  q35.1  168500001  172800000  gneg
5  q35.2  172800001  176600000  gpos25
5  q35.3  176600001  180915260  gneg
6  p11.1  58700001  61000000  acen
6  p11.2  57000001  58700000  gneg
6  p12.1  52900001  57000000  gpos100
6  p12.2  51800001  52900000  gneg
6  p12.3  46200001  51800000  gpos100
6  p21.1  40500001  46200000  gneg
6  p21.2  36600001  40500000  gpos25
6  p21.31  33500001  36600000  gneg
6  p21.32  32100001  33500000  gpos25
6  p21.33  30400001  32100000  gneg
6  p22.1  27000001  30400000  gpos50
6  p22.2  25200001  27000000  gneg
6  p22.3  15200001  25200000  gpos75
6  p23  13400001  15200000  gneg
6  p24.1  11600001  13400000  gpos25
6  p24.2  10600001  11600000  gneg
6  p24.3  7100001  10600000  gpos50
6  p25.1  4200001  7100000  gneg
6  p25.2  2300001  4200000  gpos25
6  p25.3  1  2300000  gneg
6  q11.1  61000001  63300000  acen
6  q11.2  63300001  63400000  gneg
6  q12  63400001  70000000  gpos100
6  q13  70000001  75900000  gneg
6  q14.1  75900001  83900000  gpos50
6  q14.2  83900001  84900000  gneg
6  q14.3  84900001  88000000  gpos50
6  q15  88000001  93100000  gneg
6  q16.1  93100001  99500000  gpos100
6  q16.2  99500001  100600000  gneg
6  q16.3  100600001  105500000  gpos100
6  q21  105500001  114600000  gneg
6  q22.1  114600001  118300000  gpos75
6  q22.2  118300001  118500000  gneg
6  q22.31  118500001  126100000  gpos100
6  q22.32  126100001  127100000  gneg
6  q22.33  127100001  130300000  gpos75
6  q23.1  130300001  131200000  gneg
6  q23.2  131200001  135200000  gpos50
6  q23.3  135200001  139000000  gneg
6  q24.1  139000001  142800000  gpos75
6  q24.2  142800001  145600000  gneg
6  q24.3  145600001  149000000  gpos75
6  q25.1  149000001  152500000  gneg
6  q25.2  152500001  155500000  gpos50
6  q25.3  155500001  161000000  gneg
6  q26  161000001  164500000  gpos50
6  q27  164500001  171115067  gneg
7  p11.1  58000001  59900000  acen
7  p11.2  54000001  58000000  gneg
7  p12.1  50500001  54000000  gpos75
7  p12.2  49000001  50500000  gneg
7  p12.3  45400001  49000000  gpos75
7  p13  43300001  45400000  gneg
7  p14.1  37200001  43300000  gpos75
7  p14.2  35000001  37200000  gneg
7  p14.3  28800001  35000000  gpos75
7  p15.1  28000001  28800000  gneg
7  p15.2  25500001  28000000  gpos50
7  p15.3  20900001  25500000  gneg
7  p21.1  16500001  20900000  gpos100
7  p21.2  13800001  16500000  gneg
7  p21.3  7300001  13800000  gpos100
7  p22.1  4500001  7300000  gneg
7  p22.2  2800001  4500000  gpos25
7  p22.3  1  2800000  gneg
7  q11.1  59900001  61700000  acen
7  q11.21  61700001  67000000  gneg
7  q11.22  67000001  72200000  gpos50
7  q11.23  72200001  77500000  gneg
7  q21.11  77500001  86400000  gpos100
7  q21.12  86400001  88200000  gneg
7  q21.13  88200001  91100000  gpos75
7  q21.2  91100001  92800000  gneg
7  q21.3  92800001  98000000  gpos75
7  q22.1  98000001  103800000  gneg
7  q22.2  103800001  104500000  gpos50
7  q22.3  104500001  107400000  gneg
7  q31.1  107400001  114600000  gpos75
7  q31.2  114600001  117400000  gneg
7  q31.31  117400001  121100000  gpos75
7  q31.32  121100001  123800000  gneg
7  q31.33  123800001  127100000  gpos75
7  q32.1  127100001  129200000  gneg
7  q32.2  129200001  130400000  gpos25
7  q32.3  130400001  132600000  gneg
7  q33  132600001  138200000  gpos50
7  q34  138200001  143100000  gneg
7  q35  143100001  147900000  gpos75
7  q36.1  147900001  152600000  gneg
7  q36.2  152600001  155100000  gpos25
7  q36.3  155100001  159138663  gneg
8  p11.1  43100001  45600000  acen
8  p11.21  39700001  43100000  gneg
8  p11.22  38300001  39700000  gpos25
8  p11.23  36500001  38300000  gneg
8  p12  28800001  36500000  gpos75
8  p21.1  27400001  28800000  gneg
8  p21.2  23300001  27400000  gpos50
8  p21.3  19000001  23300000  gneg
8  p22  12700001  19000000  gpos100
8  p23.1  6200001  12700000  gneg
8  p23.2  2200001  6200000  gpos75
8  p23.3  1  2200000  gneg
8  q11.1  45600001  48100000  acen
8  q11.21  48100001  52200000  gneg
8  q11.22  52200001  52600000  gpos75
8  q11.23  52600001  55500000  gneg
8  q12.1  55500001  61600000  gpos50
8  q12.2  61600001  62200000  gneg
8  q12.3  62200001  66000000  gpos50
8  q13.1  66000001  68000000  gneg
8  q13.2  68000001  70500000  gpos50
8  q13.3  70500001  73900000  gneg
8  q21.11  73900001  78300000  gpos100
8  q21.12  78300001  80100000  gneg
8  q21.13  80100001  84600000  gpos75
8  q21.2  84600001  86900000  gneg
8  q21.3  86900001  93300000  gpos100
8  q22.1  93300001  99000000  gneg
8  q22.2  99000001  101600000  gpos25
8  q22.3  101600001  106200000  gneg
8  q23.1  106200001  110500000  gpos75
8  q23.2  110500001  112100000  gneg
8  q23.3  112100001  117700000  gpos100
8  q24.11  117700001  119200000  gneg
8  q24.12  119200001  122500000  gpos50
8  q24.13  122500001  127300000  gneg
8  q24.21  127300001  131500000  gpos50
8  q24.22  131500001  136400000  gneg
8  q24.23  136400001  139900000  gpos75
8  q24.3  139900001  146364022  gneg
9  p11.1  47300001  49000000  acen
9  p11.2  43600001  47300000  gneg
9  p12  41000001  43600000  gpos50
9  p13.1  38400001  41000000  gneg
9  p13.2  36300001  38400000  gpos25
9  p13.3  33200001  36300000  gneg
9  p21.1  28000001  33200000  gpos100
9  p21.2  25600001  28000000  gneg
9  p21.3  19900001  25600000  gpos100
9  p22.1  18500001  19900000  gneg
9  p22.2  16600001  18500000  gpos25
9  p22.3  14200001  16600000  gneg
9  p23  9000001  14200000  gpos75
9  p24.1  4600001  9000000  gneg
9  p24.2  2200001  4600000  gpos25
9  p24.3  1  2200000  gneg
9  q11  49000001  50700000  acen
9  q12  50700001  65900000  gvar
9  q13  65900001  68700000  gneg
9  q21.11  68700001  72200000  gpos25
9  q21.12  72200001  74000000  gneg
9  q21.13  74000001  79200000  gpos50
9  q21.2  79200001  81100000  gneg
9  q21.31  81100001  84100000  gpos50
9  q21.32  84100001  86900000  gneg
9  q21.33  86900001  90400000  gpos50
9  q22.1  90400001  91800000  gneg
9  q22.2  91800001  93900000  gpos25
9  q22.31  93900001  96600000  gneg
9  q22.32  96600001  99300000  gpos25
9  q22.33  99300001  102600000  gneg
9  q31.1  102600001  108200000  gpos100
9  q31.2  108200001  111300000  gneg
9  q31.3  111300001  114900000  gpos25
9  q32  114900001  117700000  gneg
9  q33.1  117700001  122500000  gpos75
9  q33.2  122500001  125800000  gneg
9  q33.3  125800001  130300000  gpos25
9  q34.11  130300001  133500000  gneg
9  q34.12  133500001  134000000  gpos25
9  q34.13  134000001  135900000  gneg
9  q34.2  135900001  137400000  gpos25
9  q34.3  137400001  141213431  gneg
10  p11.1  38000001  40200000  acen
10  p11.21  34400001  38000000  gneg
10  p11.22  31300001  34400000  gpos25
10  p11.23  29600001  31300000  gneg
10  p12.1  24600001  29600000  gpos50
10  p12.2  22600001  24600000  gneg
10  p12.31  18700001  22600000  gpos75
10  p12.32  18600001  18700000  gneg
10  p12.33  17300001  18600000  gpos75
10  p13  12200001  17300000  gneg
10  p14  6600001  12200000  gpos75
10  p15.1  3800001  6600000  gneg
10  p15.2  3000001  3800000  gpos25
10  p15.3  1  3000000  gneg
10  q11.1  40200001  42300000  acen
10  q11.21  42300001  46100000  gneg
10  q11.22  46100001  49900000  gpos25
10  q11.23  49900001  52900000  gneg
10  q21.1  52900001  61200000  gpos100
10  q21.2  61200001  64500000  gneg
10  q21.3  64500001  70600000  gpos100
10  q22.1  70600001  74900000  gneg
10  q22.2  74900001  77700000  gpos50
10  q22.3  77700001  82000000  gneg
10  q23.1  82000001  87900000  gpos100
10  q23.2  87900001  89500000  gneg
10  q23.31  89500001  92900000  gpos75
10  q23.32  92900001  94100000  gneg
10  q23.33  94100001  97000000  gpos50
10  q24.1  97000001  99300000  gneg
10  q24.2  99300001  101900000  gpos50
10  q24.31  101900001  103000000  gneg
10  q24.32  103000001  104900000  gpos25
10  q24.33  104900001  105800000  gneg
10  q25.1  105800001  111900000  gpos100
10  q25.2  111900001  114900000  gneg
10  q25.3  114900001  119100000  gpos75
10  q26.11  119100001  121700000  gneg
10  q26.12  121700001  123100000  gpos50
10  q26.13  123100001  127500000  gneg
10  q26.2  127500001  130600000  gpos50
10  q26.3  130600001  135534747  gneg
11  p11.11  51600001  53700000  acen
11  p11.12  48800001  51600000  gpos75
11  p11.2  43500001  48800000  gneg
11  p12  36400001  43500000  gpos100
11  p13  31000001  36400000  gneg
11  p14.1  27200001  31000000  gpos75
11  p14.2  26100001  27200000  gneg
11  p14.3  21700001  26100000  gpos100
11  p15.1  16200001  21700000  gneg
11  p15.2  12700001  16200000  gpos50
11  p15.3  10700001  12700000  gneg
11  p15.4  2800001  10700000  gpos50
11  p15.5  1  2800000  gneg
11  q11  53700001  55700000  acen
11  q12.1  55700001  59900000  gpos75
11  q12.2  59900001  61700000  gneg
11  q12.3  61700001  63400000  gpos25
11  q13.1  63400001  65900000  gneg
11  q13.2  65900001  68400000  gpos25
11  q13.3  68400001  70400000  gneg
11  q13.4  70400001  75200000  gpos50
11  q13.5  75200001  77100000  gneg
11  q14.1  77100001  85600000  gpos100
11  q14.2  85600001  88300000  gneg
11  q14.3  88300001  92800000  gpos100
11  q21  92800001  97200000  gneg
11  q22.1  97200001  102100000  gpos100
11  q22.2  102100001  102900000  gneg
11  q22.3  102900001  110400000  gpos100
11  q23.1  110400001  112500000  gneg
11  q23.2  112500001  114500000  gpos50
11  q23.3  114500001  121200000  gneg
11  q24.1  121200001  123900000  gpos50
11  q24.2  123900001  127800000  gneg
11  q24.3  127800001  130800000  gpos50
11  q25  130800001  135006516  gneg
12  p11.1  33300001  35800000  acen
12  p11.21  30700001  33300000  gneg
12  p11.22  27800001  30700000  gpos50
12  p11.23  26500001  27800000  gneg
12  p12.1  21300001  26500000  gpos100
12  p12.2  20000001  21300000  gneg
12  p12.3  14800001  20000000  gpos100
12  p13.1  12800001  14800000  gneg
12  p13.2  10100001  12800000  gpos75
12  p13.31  5400001  10100000  gneg
12  p13.32  3300001  5400000  gpos25
12  p13.33  1  3300000  gneg
12  q11  35800001  38200000  acen
12  q12  38200001  46400000  gpos100
12  q13.11  46400001  49100000  gneg
12  q13.12  49100001  51500000  gpos25
12  q13.13  51500001  54900000  gneg
12  q13.2  54900001  56600000  gpos25
12  q13.3  56600001  58100000  gneg
12  q14.1  58100001  63100000  gpos75
12  q14.2  63100001  65100000  gneg
12  q14.3  65100001  67700000  gpos50
12  q15  67700001  71500000  gneg
12  q21.1  71500001  75700000  gpos75
12  q21.2  75700001  80300000  gneg
12  q21.31  80300001  86700000  gpos100
12  q21.32  86700001  89000000  gneg
12  q21.33  89000001  92600000  gpos100
12  q22  92600001  96200000  gneg
12  q23.1  96200001  101600000  gpos75
12  q23.2  101600001  103800000  gneg
12  q23.3  103800001  109000000  gpos50
12  q24.11  109000001  111700000  gneg
12  q24.12  111700001  112300000  gpos25
12  q24.13  112300001  114300000  gneg
12  q24.21  114300001  116800000  gpos50
12  q24.22  116800001  118100000  gneg
12  q24.23  118100001  120700000  gpos50
12  q24.31  120700001  125900000  gneg
12  q24.32  125900001  129300000  gpos50
12  q24.33  129300001  133851895  gneg
13  p11.1  16300001  17900000  acen
13  p11.2  10000001  16300000  gvar
13  p12  4500001  10000000  stalk
13  p13  1  4500000  gvar
13  q11  17900001  19500000  acen
13  q12.11  19500001  23300000  gneg
13  q12.12  23300001  25500000  gpos25
13  q12.13  25500001  27800000  gneg
13  q12.2  27800001  28900000  gpos25
13  q12.3  28900001  32200000  gneg
13  q13.1  32200001  34000000  gpos50
13  q13.2  34000001  35500000  gneg
13  q13.3  35500001  40100000  gpos75
13  q14.11  40100001  45200000  gneg
13  q14.12  45200001  45800000  gpos25
13  q14.13  45800001  47300000  gneg
13  q14.2  47300001  50900000  gpos50
13  q14.3  50900001  55300000  gneg
13  q21.1  55300001  59600000  gpos100
13  q21.2  59600001  62300000  gneg
13  q21.31  62300001  65700000  gpos75
13  q21.32  65700001  68600000  gneg
13  q21.33  68600001  73300000  gpos100
13  q22.1  73300001  75400000  gneg
13  q22.2  75400001  77200000  gpos50
13  q22.3  77200001  79000000  gneg
13  q31.1  79000001  87700000  gpos100
13  q31.2  87700001  90000000  gneg
13  q31.3  90000001  95000000  gpos100
13  q32.1  95000001  98200000  gneg
13  q32.2  98200001  99300000  gpos25
13  q32.3  99300001  101700000  gneg
13  q33.1  101700001  104800000  gpos100
13  q33.2  104800001  107000000  gneg
13  q33.3  107000001  110300000  gpos100
13  q34  110300001  115169878  gneg
14  p11.1  16100001  17600000  acen
14  p11.2  8100001  16100000  gvar
14  p12  3700001  8100000  stalk
14  p13  1  3700000  gvar
14  q11.1  17600001  19100000  acen
14  q11.2  19100001  24600000  gneg
14  q12  24600001  33300000  gpos100
14  q13.1  33300001  35300000  gneg
14  q13.2  35300001  36600000  gpos50
14  q13.3  36600001  37800000  gneg
14  q21.1  37800001  43500000  gpos100
14  q21.2  43500001  47200000  gneg
14  q21.3  47200001  50900000  gpos100
14  q22.1  50900001  54100000  gneg
14  q22.2  54100001  55500000  gpos25
14  q22.3  55500001  58100000  gneg
14  q23.1  58100001  62100000  gpos75
14  q23.2  62100001  64800000  gneg
14  q23.3  64800001  67900000  gpos50
14  q24.1  67900001  70200000  gneg
14  q24.2  70200001  73800000  gpos50
14  q24.3  73800001  79300000  gneg
14  q31.1  79300001  83600000  gpos100
14  q31.2  83600001  84900000  gneg
14  q31.3  84900001  89800000  gpos100
14  q32.11  89800001  91900000  gneg
14  q32.12  91900001  94700000  gpos25
14  q32.13  94700001  96300000  gneg
14  q32.2  96300001  101400000  gpos50
14  q32.31  101400001  103200000  gneg
14  q32.32  103200001  104000000  gpos50
14  q32.33  104000001  107349540  gneg
15  p11.1  15800001  19000000  acen
15  p11.2  8700001  15800000  gvar
15  p12  3900001  8700000  stalk
15  p13  1  3900000  gvar
15  q11.1  19000001  20700000  acen
15  q11.2  20700001  25700000  gneg
15  q12  25700001  28100000  gpos50
15  q13.1  28100001  30300000  gneg
15  q13.2  30300001  31200000  gpos50
15  q13.3  31200001  33600000  gneg
15  q14  33600001  40100000  gpos75
15  q15.1  40100001  42800000  gneg
15  q15.2  42800001  43600000  gpos25
15  q15.3  43600001  44800000  gneg
15  q21.1  44800001  49500000  gpos75
15  q21.2  49500001  52900000  gneg
15  q21.3  52900001  59100000  gpos75
15  q22.1  59100001  59300000  gneg
15  q22.2  59300001  63700000  gpos25
15  q22.31  63700001  67200000  gneg
15  q22.32  67200001  67300000  gpos25
15  q22.33  67300001  67500000  gneg
15  q23  67500001  72700000  gpos25
15  q24.1  72700001  75200000  gneg
15  q24.2  75200001  76600000  gpos25
15  q24.3  76600001  78300000  gneg
15  q25.1  78300001  81700000  gpos50
15  q25.2  81700001  85200000  gneg
15  q25.3  85200001  89100000  gpos50
15  q26.1  89100001  94300000  gneg
15  q26.2  94300001  98500000  gpos50
15  q26.3  98500001  102531392  gneg
16  p11.1  34600001  36600000  acen
16  p11.2  28100001  34600000  gneg
16  p12.1  24200001  28100000  gpos50
16  p12.2  21200001  24200000  gneg
16  p12.3  16800001  21200000  gpos50
16  p13.11  14800001  16800000  gneg
16  p13.12  12600001  14800000  gpos50
16  p13.13  10500001  12600000  gneg
16  p13.2  7900001  10500000  gpos50
16  p13.3  1  7900000  gneg
16  q11.1  36600001  38600000  acen
16  q11.2  38600001  47000000  gvar
16  q12.1  47000001  52600000  gneg
16  q12.2  52600001  56700000  gpos50
16  q13  56700001  57400000  gneg
16  q21  57400001  66700000  gpos100
16  q22.1  66700001  70800000  gneg
16  q22.2  70800001  72900000  gpos50
16  q22.3  72900001  74100000  gneg
16  q23.1  74100001  79200000  gpos75
16  q23.2  79200001  81700000  gneg
16  q23.3  81700001  84200000  gpos50
16  q24.1  84200001  87100000  gneg
16  q24.2  87100001  88700000  gpos25
16  q24.3  88700001  90354753  gneg
17  p11.1  22200001  24000000  acen
17  p11.2  16000001  22200000  gneg
17  p12  10700001  16000000  gpos75
17  p13.1  6500001  10700000  gneg
17  p13.2  3300001  6500000  gpos50
17  p13.3  1  3300000  gneg
17  q11.1  24000001  25800000  acen
17  q11.2  25800001  31800000  gneg
17  q12  31800001  38100000  gpos50
17  q21.1  38100001  38400000  gneg
17  q21.2  38400001  40900000  gpos25
17  q21.31  40900001  44900000  gneg
17  q21.32  44900001  47400000  gpos25
17  q21.33  47400001  50200000  gneg
17  q22  50200001  57600000  gpos75
17  q23.1  57600001  58300000  gneg
17  q23.2  58300001  61100000  gpos75
17  q23.3  61100001  62600000  gneg
17  q24.1  62600001  64200000  gpos50
17  q24.2  64200001  67100000  gneg
17  q24.3  67100001  70900000  gpos75
17  q25.1  70900001  74800000  gneg
17  q25.2  74800001  75300000  gpos25
17  q25.3  75300001  81195210  gneg
18  p11.1  15400001  17200000  acen
18  p11.21  10900001  15400000  gneg
18  p11.22  8500001  10900000  gpos25
18  p11.23  7100001  8500000  gneg
18  p11.31  2900001  7100000  gpos50
18  p11.32  1  2900000  gneg
18  q11.1  17200001  19000000  acen
18  q11.2  19000001  25000000  gneg
18  q12.1  25000001  32700000  gpos100
18  q12.2  32700001  37200000  gneg
18  q12.3  37200001  43500000  gpos75
18  q21.1  43500001  48200000  gneg
18  q21.2  48200001  53800000  gpos75
18  q21.31  53800001  56200000  gneg
18  q21.32  56200001  59000000  gpos50
18  q21.33  59000001  61600000  gneg
18  q22.1  61600001  66800000  gpos100
18  q22.2  66800001  68700000  gneg
18  q22.3  68700001  73100000  gpos25
18  q23  73100001  78077248  gneg
19  p11  24400001  26500000  acen
19  p12  20000001  24400000  gvar
19  p13.11  16300001  20000000  gneg
19  p13.12  14000001  16300000  gpos25
19  p13.13  13900001  14000000  gneg
19  p13.2  6900001  13900000  gpos25
19  p13.3  1  6900000  gneg
19  q11  26500001  28600000  acen
19  q12  28600001  32400000  gvar
19  q13.11  32400001  35500000  gneg
19  q13.12  35500001  38300000  gpos25
19  q13.13  38300001  38700000  gneg
19  q13.2  38700001  43400000  gpos25
19  q13.31  43400001  45200000  gneg
19  q13.32  45200001  48000000  gpos25
19  q13.33  48000001  51400000  gneg
19  q13.41  51400001  53600000  gpos25
19  q13.42  53600001  56300000  gneg
19  q13.43  56300001  59128983  gpos25
20  p11.1  25600001  27500000  acen
20  p11.21  22300001  25600000  gneg
20  p11.22  21300001  22300000  gpos25
20  p11.23  17900001  21300000  gneg
20  p12.1  12100001  17900000  gpos75
20  p12.2  9200001  12100000  gneg
20  p12.3  5100001  9200000  gpos75
20  p13  1  5100000  gneg
20  q11.1  27500001  29400000  acen
20  q11.21  29400001  32100000  gneg
20  q11.22  32100001  34400000  gpos25
20  q11.23  34400001  37600000  gneg
20  q12  37600001  41700000  gpos75
20  q13.11  41700001  42100000  gneg
20  q13.12  42100001  46400000  gpos25
20  q13.13  46400001  49800000  gneg
20  q13.2  49800001  55000000  gpos75
20  q13.31  55000001  56500000  gneg
20  q13.32  56500001  58400000  gpos50
20  q13.33  58400001  63025520  gneg
21  p11.1  10900001  13200000  acen
21  p11.2  6800001  10900000  gvar
21  p12  2800001  6800000  stalk
21  p13  1  2800000  gvar
21  q11.1  13200001  14300000  acen
21  q11.2  14300001  16400000  gneg
21  q21.1  16400001  24000000  gpos100
21  q21.2  24000001  26800000  gneg
21  q21.3  26800001  31500000  gpos75
21  q22.11  31500001  35800000  gneg
21  q22.12  35800001  37800000  gpos50
21  q22.13  37800001  39700000  gneg
21  q22.2  39700001  42600000  gpos50
21  q22.3  42600001  48129895  gneg
22  p11.1  12200001  14700000  acen
22  p11.2  8300001  12200000  gvar
22  p12  3800001  8300000  stalk
22  p13  1  3800000  gvar
22  q11.1  14700001  17900000  acen
22  q11.21  17900001  22200000  gneg
22  q11.22  22200001  23500000  gpos25
22  q11.23  23500001  25900000  gneg
22  q12.1  25900001  29600000  gpos50
22  q12.2  29600001  32200000  gneg
22  q12.3  32200001  37600000  gpos50
22  q13.1  37600001  41000000  gneg
22  q13.2  41000001  44200000  gpos50
22  q13.31  44200001  48400000  gneg
22  q13.32  48400001  49400000  gpos50
22  q13.33  49400001  51304566  gneg
X  p11.1  58100001  60600000  acen
X  p11.21  54800001  58100000  gneg
X  p11.22  49800001  54800000  gpos25
X  p11.23  46400001  49800000  gneg
X  p11.3  42400001  46400000  gpos75
X  p11.4  37600001  42400000  gneg
X  p21.1  31500001  37600000  gpos100
X  p21.2  29300001  31500000  gneg
X  p21.3  24900001  29300000  gpos100
X  p22.11  21900001  24900000  gneg
X  p22.12  19300001  21900000  gpos50
X  p22.13  17100001  19300000  gneg
X  p22.2  9500001  17100000  gpos50
X  p22.31  6000001  9500000  gneg
X  p22.32  4300001  6000000  gpos50
X  p22.33  1  4300000  gneg
X  q11.1  60600001  63000000  acen
X  q11.2  63000001  64600000  gneg
X  q12  64600001  67800000  gpos50
X  q13.1  67800001  71800000  gneg
X  q13.2  71800001  73900000  gpos50
X  q13.3  73900001  76000000  gneg
X  q21.1  76000001  84600000  gpos100
X  q21.2  84600001  86200000  gneg
X  q21.31  86200001  91800000  gpos100
X  q21.32  91800001  93500000  gneg
X  q21.33  93500001  98300000  gpos75
X  q22.1  98300001  102600000  gneg
X  q22.2  102600001  103700000  gpos50
X  q22.3  103700001  108700000  gneg
X  q23  108700001  116500000  gpos75
X  q24  116500001  120900000  gneg
X  q25  120900001  128700000  gpos100
X  q26.1  128700001  130400000  gneg
X  q26.2  130400001  133600000  gpos25
X  q26.3  133600001  138000000  gneg
X  q27.1  138000001  140300000  gpos75
X  q27.2  140300001  142100000  gneg
X  q27.3  142100001  147100000  gpos100
X  q28  147100001  155270560  gneg
Y  p11.1  11600001  12500000  acen
Y  p11.2  3000001  11600000  gneg
Y  p11.31  2500001  3000000  gpos50
Y  p11.32  1  2500000  gneg
Y  q11.1  12500001  13400000  acen
Y  q11.21  13400001  15100000  gneg
Y  q11.221  15100001  19800000  gpos50
Y  q11.222  19800001  22100000  gneg
Y  q11.223  22100001  26200000  gpos50
Y  q11.23  26200001  28800000  gneg
Y  q12  28800001  59373566  gvar

Symbols used:

The following symbols are often used with band numbers when describing changes in the karyogram, eg. of cancer cells in ISCN notation.

 , 	Separates chromosome modal number, sex chromosomes, 
        and chromosome abnormalities

 - 	Loss of a chromosome

 ( ) 	Surround structurally altered chromosomes and breakpoints

 + 	Gain of a chromosome

 ++     Multiple signals on one chromosome

 ; 	Separates rearranged chromosomes and breakpoints involving
        more than one chromosome

 / 	Separates cell lines or clones

 // 	Separates recipient and donor cell lines in bone marrow
        transplants

 ~      approximation

 x      multiple copies of chromosomes or regions

 .      Sperates multiple techniques

 amp    amplification

 arr    microarray data

 dim    diminished fluorescence ratio intensity: deletion

 del 	Deletion

 der 	Derivative chromosome (used when only one chromosome from
        a translocation is present, or when one chromosome has two
        or more structural abnormalities).
        Alternative description:
        Structurally rearranged chromosome generated either by a 
        rearrangement involving two or more chromosomes or by multiple
        aberrations within a single chromosome (e.g. an inversion and a
        deletion of the same chromosome, or deletions in both arms of a
        single chromosome).[1] The term always refers to the chromosome
        that has an intact centromere.

 dic 	Dicentric chromosome

 dn 	Chromosomal abnormality not inherited from parents (de novo)

 dup 	Duplication of a portion of a chromosome

 enh 	Enhanced fluorescence ratio intensity: duplication

 fra 	Fragile site (usually used with Fragile-X syndrome)

 h 	Heterochromatic region of chromosome

 hlpa   Multiple ligation-dependent probe amplifications

 hmz    Homozygosity

 htz    Heterozygosity

 i 	Isochromosome (both arms of the chromosome are the same)

 ins 	Insertion of a portion of a chromosome

 inv 	Inversion

 .ish 	Precedes karyotype results from fluorescence in situ
        hybridization (FISH) analysis

 mar 	Marker chromosome (unidentifiable piece of chromosome)

 mat 	Maternally derived chromosome rearrangement

 p 	Short arm of a chromosome

 pat 	Paternally derived chromosome rearrangement

 psu dic 	Only one centromere is active (pseudo dicentric)

 q 	Long arm of a chromosome

 r 	Ring chromosome

 t 	Translocation

 ter 	Terminal end of arm (i.e. 2qter - end of the long arm
        of chromosome 2)

 tri	Trisomy

 trp 	Triplication of a portion of a chromosome 

The software CyDAS seems to be able to work with this kind of karyotype data and there is also a discussion about shortcomings of the nomenclature. (Some of the issues might have been fixed in the mean times.)
There is also a publication by Mascarello et al. about the shortcomings of the system, shown by comparisons how different clinicians used it in a survey analysis. Up to 50% of the notations used for specific cases were incorrect and only 8% of participants used the exact same string to describe a trisomy 21 in uncultured amniocytes.

Sources and further reading:

Encode pilot regions

July 28th, 2011

This is the list of genomic regions that was analysed as the 1% of the human genome in the ENCODE pilot phase. (The main phase of ENCODE is looking at the entire human genome.) The coordinates are for assembly NCBI36 (hg18).
See also the entry about ENCODE and the UCSC pages.

Name Chr. Start End Description
ENr231 1 149424685 149924684 Random Picks
ENr131 2 234156564 234656627 Random Picks
ENr331 2 219985590 220485589 Random Picks
ENr112 2 51512209 52012208 Random Picks
ENr121 2 118011044 118511043 Random Picks
ENr113 4 118466104 118966103 Random Picks
ENr212 5 141880151 142380150 Random Picks
ENm002 5 131284314 132284313 Manual Picks:Interleukin
ENr221 5 55871007 56371006 Random Picks
ENr222 6 132218540 132718539 Random Picks
ENr223 6 73789953 74289952 Random Picks
ENr323 6 108371397 108871396 Random Picks
ENr334 6 41405895 41905894 Random Picks
ENm013 7 89621625 90736048 Manual Picks
ENm001 7 115597757 117475182 Manual Picks:CFTR
ENm010 7 26924046 27424045 Manual Picks:HOXA
ENm012 7 113720369 114720368 Manual Picks:FOXP2
ENm014 7 125865892 127029088 Manual Picks
ENr321 8 118882221 119382220 Random Picks
ENr232 9 130725123 131225122 Random Picks
ENr114 10 55153819 55653818 Random Picks
ENr312 11 130604798 131104797 Random Picks
ENr332 11 63940889 64440888 Random Picks
ENm009 11 4730996 5732587 Manual Picks:Beta
ENm011 11 1699992 2306039 Manual Picks:1GF2/H19
ENm003 11 115962316 116462315 Manual Picks:Apo
ENr123 12 38626477 39126476 Random Picks
ENr111 13 29418016 29918015 Random Picks
ENr132 13 112338065 112838064 Random Picks
ENr311 14 52947076 53447075 Random Picks
ENr322 14 98458224 98958223 Random Picks
ENr233 15 41520089 42020088 Random Picks
ENm008 16 1 500000 Manual Picks:Alpha
ENr313 16 60833950 61333949 Random Picks
ENr211 16 25780428 26280428 Random Picks
ENr213 18 23719232 24219231 Random Picks
ENr122 18 59412301 59912300 Random Picks
ENm007 19 59023585 60024460 Manual Picks:Chr19
ENr333 20 33304929 33804928 Random Picks
ENr133 21 39244467 39744466 Random Picks
ENm005 21 32668237 34364221 Manual Picks:Chr21
ENm004 22 30133954 31833953 Manual Picks:Chr22
ENr324 X 122609996 123109995 Random Picks
ENm006 X 152767492 154063081 Manual Picks:ChrX

Public Ensembl databases

July 5th, 2011

A quick reminder of the specifications to connect to the public Ensembl mySQL databases:

Database Server Port
Ensembl (v 24-47)
ensembldb.ensembl.org††
3306
Ensembl (v 48 and above)
ensembldb.ensembl.org 5306
Ensembl Mart martdb.ensembl.org 5316
Ensembl Genomes mysql.ebi.ac.uk 4157
Ensembl (curr. v) in US cloud useastdb.ensembl.org 5306

user = "anonymous"

pass = ""

mysql commandline for connection:

Code

mysql -uanonymous -hensembldb.ensembl.org -P5306