[ensembl-dev] HG883_PATCH

Tue Mar 25 14:43:11 GMT 2014

Hi,

The gtf file:

ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz

contains the below unique list of regions. What are these categories of
patches refer to? Are these all fix patches or also novel ones? GL,
HG_PATCH, HG_HG_PATCH, HG_HG_NOVEL_TEST, HSCHR, HSCHR_CTG, HSCHR_MHC,
HSCHR_LRC, HSCHR_HG.

Thanks,

Genomeo

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
GL000191.1
GL000192.1
GL000193.1
GL000194.1
GL000195.1
GL000196.1
GL000199.1
GL000201.1
GL000204.1
GL000205.1
GL000209.1
GL000211.1
GL000212.1
GL000213.1
GL000215.1
GL000216.1
GL000218.1
GL000219.1
GL000220.1
GL000221.1
GL000222.1
GL000223.1
GL000224.1
GL000225.1
GL000228.1
GL000229.1
GL000230.1
GL000231.1
GL000233.1
GL000236.1
GL000237.1
GL000240.1
GL000241.1
GL000242.1
GL000243.1
GL000247.1
HG1007_PATCH
HG1032_PATCH
HG104_HG975_PATCH
HG1063_PATCH
HG1074_PATCH
HG1079_PATCH
HG1082_HG167_PATCH
HG1091_PATCH
HG1133_PATCH
HG1146_PATCH
HG115_PATCH
HG1208_PATCH
HG1211_PATCH
HG122_PATCH
HG1257_PATCH
HG1287_PATCH
HG1292_PATCH
HG1293_PATCH
HG1304_PATCH
HG1308_PATCH
HG1322_PATCH
HG1350_HG959_PATCH
HG1423_PATCH
HG1424_PATCH
HG1425_PATCH
HG1426_PATCH
HG142_HG150_NOVEL_TEST
HG1433_PATCH
HG1434_PATCH
HG1435_PATCH
HG1436_HG1432_PATCH
HG1437_PATCH
HG1438_PATCH
HG1439_PATCH
HG1440_PATCH
HG1441_PATCH
HG1442_PATCH
HG1443_HG1444_PATCH
HG144_PATCH
HG1453_PATCH
HG1458_PATCH
HG1459_PATCH
HG1462_PATCH
HG1463_PATCH
HG1472_PATCH
HG1479_PATCH
HG1486_PATCH
HG1487_PATCH
HG1488_PATCH
HG1490_PATCH
HG1497_PATCH
HG14_PATCH
HG1500_PATCH
HG1501_PATCH
HG1502_PATCH
HG151_NOVEL_TEST
HG1591_PATCH
HG1592_PATCH
HG1595_PATCH
HG1699_PATCH
HG174_HG254_PATCH
HG183_PATCH
HG185_PATCH
HG186_PATCH
HG193_PATCH
HG19_PATCH
HG237_PATCH
HG243_PATCH
HG256_PATCH
HG271_PATCH
HG27_PATCH
HG280_PATCH
HG281_PATCH
HG299_PATCH
HG29_PATCH
HG305_PATCH
HG306_PATCH
HG311_PATCH
HG325_PATCH
HG329_PATCH
HG339_PATCH
HG344_PATCH
HG348_PATCH
HG357_PATCH
HG375_PATCH
HG385_PATCH
HG388_HG400_PATCH
HG414_PATCH
HG417_PATCH
HG418_PATCH
HG444_PATCH
HG480_HG481_PATCH
HG497_PATCH
HG506_HG507_HG1000_PATCH
HG50_PATCH
HG531_PATCH
HG536_PATCH
HG544_PATCH
HG686_PATCH
HG706_PATCH
HG729_PATCH
HG730_PATCH
HG736_PATCH
HG745_PATCH
HG747_PATCH
HG748_PATCH
HG75_PATCH
HG79_PATCH
HG7_PATCH
HG858_PATCH
HG865_PATCH
HG871_PATCH
HG873_PATCH
HG883_PATCH
HG905_PATCH
HG944_PATCH
HG946_PATCH
HG953_PATCH
HG957_PATCH
HG962_PATCH
HG971_PATCH
HG979_PATCH
HG987_PATCH
HG989_PATCH
HG990_PATCH
HG991_PATCH
HG996_PATCH
HG998_1_PATCH
HG998_2_PATCH
HG999_1_PATCH
HG999_2_PATCH
HSCHR10_1_CTG2
HSCHR10_1_CTG5
HSCHR1_1_CTG31
HSCHR12_1_CTG1
HSCHR12_1_CTG2_1
HSCHR12_1_CTG5
HSCHR12_2_CTG2
HSCHR12_2_CTG2_1
HSCHR12_3_CTG2_1
HSCHR1_2_CTG31
HSCHR1_3_CTG31
HSCHR15_1_CTG4
HSCHR15_1_CTG8
HSCHR16_1_CTG3_1
HSCHR16_2_CTG3_1
HSCHR17_1
HSCHR17_1_CTG1
HSCHR17_1_CTG4
HSCHR17_2_CTG4
HSCHR17_3_CTG4
HSCHR17_4_CTG4
HSCHR17_5_CTG4
HSCHR17_6_CTG4
HSCHR18_1_CTG1_1
HSCHR18_1_CTG2_1
HSCHR18_2_CTG2
HSCHR18_2_CTG2_1
HSCHR19_1_CTG3
HSCHR19_1_CTG3_1
HSCHR19_2_CTG3
HSCHR19_3_CTG3
HSCHR19LRC_COX1_CTG1
HSCHR19LRC_COX2_CTG1
HSCHR19LRC_LRC_I_CTG1
HSCHR19LRC_LRC_J_CTG1
HSCHR19LRC_LRC_S_CTG1
HSCHR19LRC_LRC_T_CTG1
HSCHR19LRC_PGF1_CTG1
HSCHR19LRC_PGF2_CTG1
HSCHR20_1_CTG1
HSCHR21_2_CTG1_1
HSCHR21_3_CTG1_1
HSCHR21_4_CTG1_1
HSCHR2_1_CTG1
HSCHR2_1_CTG12
HSCHR22_1_CTG1
HSCHR22_1_CTG2
HSCHR22_2_CTG1
HSCHR2_2_CTG12
HSCHR3_1_CTG1
HSCHR3_1_CTG2_1
HSCHR4_1
HSCHR4_1_CTG12
HSCHR4_1_CTG6
HSCHR4_2_CTG9
HSCHR5_1_CTG1
HSCHR5_1_CTG2
HSCHR5_1_CTG5
HSCHR5_2_CTG1
HSCHR5_3_CTG1
HSCHR6_1_CTG5
HSCHR6_MHC_APD
HSCHR6_MHC_COX
HSCHR6_MHC_DBB
HSCHR6_MHC_MANN
HSCHR6_MHC_MCF
HSCHR6_MHC_QBL
HSCHR6_MHC_SSTO
HSCHR7_1_CTG6
HSCHR9_1_CTG1
HSCHR9_1_CTG35
HSCHR9_2_CTG35
HSCHR9_3_CTG35
MT
X
Y

On 24 March 2014 07:58, mag <mr6 at ebi.ac.uk> wrote:

> Hi Enrico,
>
> HG883_PATCH is indeed a patch.
> The human reference assembly contains fix patches, which attempt to
> correct sequencing errors in the primary assembly, as well as novel
> patches, or haplotypes.
> More information here:
> http://www.ensembl.org/Help/Glossary?id=297
>
> HG883_PATCH is located on chromosome 17, as can be seen on this view:
> http://www.ensembl.org/Homo_sapiens/Location/View?db=core;
> r=HG883_PATCH:26729129-26731068
> If you click outside of the green region, it will tell you which
> chromosome you are on.
>
> LRGs are Locus Reference Genomic.
> These provide an assembly-independent gene location and are mainly used by
> the diagnostic community.
> More information here:
> http://www.ensembl.org/Help/Glossary?id=406
>
> To ensure the uniqueness of a sequence, you should align it against the
> primary assembly, hence excluding all alternative sequences.
> On our ftp site (ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/
> dna), the sequence is called Homo_sapiens.GRCh37.75.dna_sm.
> primary_assembly.fa
>
>
> Hope that helps,
> Magali
>
>
> On 24/03/2014 05:33, Enrico Rubagotti wrote:
>
>> Hi all,
>> I wish to ensure the uniqueness of ENST00000003834 in the human genome.
>> To achieve this objective  I blasted ENST00000003834 (identity value
>> =100%) over the entire GRCh37.p13 and the result was aligned to the Chr 17,
>> and HG883_PATCH and LRG_183.
>> HG883_PATCH looks like a patch of the human genome, to which chromosome
>> it refers?
>> What is LRG_183?
>>
>> Please find below the result from blast
>>
>> Query=  ENSG00000004139|ENST00000003834|26691378|26728065|17
>> Length=2916
>> Score     E
>> Sequences producing significant alignments: (Bits)  Value
>>
>> ENSG00000004139|ENST00000003834|26691378|26728065|17 5385    0.0
>> LRG_183|LRG_183t1|5001|16567|LRG_183 3701    0.0
>> ENSG00000076351|ENST00000583295|26721661|26734215|17 3701    0.0
>> ENSG00000076351|ENST00000584729|26721661|26734215|17 3701    0.0
>> ENSG00000267556|ENST00000591663|26691378|26725182|HG883_PATCH 1615    0.0
>> ENSG00000267556|ENST00000585482|26691378|26725182|HG883_PATCH 1242    0.0
>> ENSG00000004139|ENST00000578128|26691378|26728065|17 1242    0.0
>> ENSG00000004139|ENST00000579593|26691378|26728065|17 1227    0.0
>> ENSG00000267556|ENST00000585569|26691378|26725182|HG883_PATCH 660    0.0
>> ENSG00000004139|ENST00000577870|26691378|26728065|17 660    0.0
>> ENSG00000267556|ENST00000589014|26691378|26725182|HG883_PATCH 278
>>  2e-72
>> ENSG00000004139|ENST00000582323|26691378|26728065|17 278    2e-72
>> ENSG00000267556|ENST00000591907|26691378|26725182|HG883_PATCH 154
>>  3e-35
>>
>> Kind regards,
>>
>> Enrico
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>

-- 
G.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140325/55bd4120/attachment.html>