[ensembl-dev] HG883_PATCH

Mon Mar 31 17:37:25 BST 2014

Hi,

Any response from the developers on the question about the patches please?

Regards,

G.

On 25 March 2014 14:43, Genomeo Dev <genomeodev at gmail.com> wrote:

> 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.
>

-- 
G.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140331/6f4e79e6/attachment.html>