<div dir="ltr">Hi,<div><br></div><div>Any response from the developers on the question about the patches please?</div><div><br></div><div>Regards,</div><div><br></div><div>G.</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On 25 March 2014 14:43, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi,<div><br></div><div>The gtf file:</div><div><br></div><div><a href="ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz" target="_blank">ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz</a><br>
</div><div><br></div><div>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.</div>
<div><br></div><div>Thanks,</div><div><br></div><div>Genomeo</div><div><br></div><div><div>1</div><div>2</div><div>3</div><div>4</div><div>5</div><div>6</div><div>7</div><div>8</div><div>9</div><div>10</div><div>11</div>
<div>
12</div><div>13</div><div>14</div><div>15</div><div>16</div><div>17</div><div>18</div><div>19</div><div>20</div><div>21</div><div>22</div><div>GL000191.1</div><div>GL000192.1</div><div>GL000193.1</div><div>GL000194.1</div>
<div>GL000195.1</div><div>GL000196.1</div><div>GL000199.1</div><div>GL000201.1</div><div>GL000204.1</div><div>GL000205.1</div><div>GL000209.1</div><div>GL000211.1</div><div>GL000212.1</div><div>GL000213.1</div><div>GL000215.1</div>
<div>GL000216.1</div><div>GL000218.1</div><div>GL000219.1</div><div>GL000220.1</div><div>GL000221.1</div><div>GL000222.1</div><div>GL000223.1</div><div>GL000224.1</div><div>GL000225.1</div><div>GL000228.1</div><div>GL000229.1</div>
<div>GL000230.1</div><div>GL000231.1</div><div>GL000233.1</div><div>GL000236.1</div><div>GL000237.1</div><div>GL000240.1</div><div>GL000241.1</div><div>GL000242.1</div><div>GL000243.1</div><div>GL000247.1</div><div>HG1007_PATCH</div>
<div>HG1032_PATCH</div><div>HG104_HG975_PATCH</div><div>HG1063_PATCH</div><div>HG1074_PATCH</div><div>HG1079_PATCH</div><div>HG1082_HG167_PATCH</div><div>HG1091_PATCH</div><div>HG1133_PATCH</div><div>HG1146_PATCH</div><div>
HG115_PATCH</div><div>HG1208_PATCH</div><div>HG1211_PATCH</div><div>HG122_PATCH</div><div>HG1257_PATCH</div><div>HG1287_PATCH</div><div>HG1292_PATCH</div><div>HG1293_PATCH</div><div>HG1304_PATCH</div><div>HG1308_PATCH</div>
<div>HG1322_PATCH</div><div>HG1350_HG959_PATCH</div><div>HG1423_PATCH</div><div>HG1424_PATCH</div><div>HG1425_PATCH</div><div>HG1426_PATCH</div><div>HG142_HG150_NOVEL_TEST</div><div>HG1433_PATCH</div><div>HG1434_PATCH</div>
<div>HG1435_PATCH</div><div>HG1436_HG1432_PATCH</div><div>HG1437_PATCH</div><div>HG1438_PATCH</div><div>HG1439_PATCH</div><div>HG1440_PATCH</div><div>HG1441_PATCH</div><div>HG1442_PATCH</div><div>HG1443_HG1444_PATCH</div>
<div>HG144_PATCH</div><div>HG1453_PATCH</div><div>HG1458_PATCH</div><div>HG1459_PATCH</div><div>HG1462_PATCH</div><div>HG1463_PATCH</div><div>HG1472_PATCH</div><div>HG1479_PATCH</div><div>HG1486_PATCH</div><div>HG1487_PATCH</div>
<div>HG1488_PATCH</div><div>HG1490_PATCH</div><div>HG1497_PATCH</div><div>HG14_PATCH</div><div>HG1500_PATCH</div><div>HG1501_PATCH</div><div>HG1502_PATCH</div><div>HG151_NOVEL_TEST</div><div>HG1591_PATCH</div><div>HG1592_PATCH</div>
<div>HG1595_PATCH</div><div>HG1699_PATCH</div><div>HG174_HG254_PATCH</div><div>HG183_PATCH</div><div>HG185_PATCH</div><div>HG186_PATCH</div><div>HG193_PATCH</div><div>HG19_PATCH</div><div>HG237_PATCH</div><div>HG243_PATCH</div>
<div>HG256_PATCH</div><div>HG271_PATCH</div><div>HG27_PATCH</div><div>HG280_PATCH</div><div>HG281_PATCH</div><div>HG299_PATCH</div><div>HG29_PATCH</div><div>HG305_PATCH</div><div>HG306_PATCH</div><div>HG311_PATCH</div><div>
HG325_PATCH</div><div>HG329_PATCH</div><div>HG339_PATCH</div><div>HG344_PATCH</div><div>HG348_PATCH</div><div>HG357_PATCH</div><div>HG375_PATCH</div><div>HG385_PATCH</div><div>HG388_HG400_PATCH</div><div>HG414_PATCH</div>
<div>HG417_PATCH</div><div>HG418_PATCH</div><div>HG444_PATCH</div><div>HG480_HG481_PATCH</div><div>HG497_PATCH</div><div>HG506_HG507_HG1000_PATCH</div><div>HG50_PATCH</div><div>HG531_PATCH</div><div>HG536_PATCH</div><div>
HG544_PATCH</div><div>HG686_PATCH</div><div>HG706_PATCH</div><div>HG729_PATCH</div><div>HG730_PATCH</div><div>HG736_PATCH</div><div>HG745_PATCH</div><div>HG747_PATCH</div><div>HG748_PATCH</div><div>HG75_PATCH</div><div>HG79_PATCH</div>
<div>HG7_PATCH</div><div>HG858_PATCH</div><div>HG865_PATCH</div><div>HG871_PATCH</div><div>HG873_PATCH</div><div>HG883_PATCH</div><div>HG905_PATCH</div><div>HG944_PATCH</div><div>HG946_PATCH</div><div>HG953_PATCH</div><div>
HG957_PATCH</div><div>HG962_PATCH</div><div>HG971_PATCH</div><div>HG979_PATCH</div><div>HG987_PATCH</div><div>HG989_PATCH</div><div>HG990_PATCH</div><div>HG991_PATCH</div><div>HG996_PATCH</div><div>HG998_1_PATCH</div><div>
HG998_2_PATCH</div><div>HG999_1_PATCH</div><div>HG999_2_PATCH</div><div>HSCHR10_1_CTG2</div><div>HSCHR10_1_CTG5</div><div>HSCHR1_1_CTG31</div><div>HSCHR12_1_CTG1</div><div>HSCHR12_1_CTG2_1</div><div>HSCHR12_1_CTG5</div><div>
HSCHR12_2_CTG2</div><div>HSCHR12_2_CTG2_1</div><div>HSCHR12_3_CTG2_1</div><div>HSCHR1_2_CTG31</div><div>HSCHR1_3_CTG31</div><div>HSCHR15_1_CTG4</div><div>HSCHR15_1_CTG8</div><div>HSCHR16_1_CTG3_1</div><div>HSCHR16_2_CTG3_1</div>
<div>HSCHR17_1</div><div>HSCHR17_1_CTG1</div><div>HSCHR17_1_CTG4</div><div>HSCHR17_2_CTG4</div><div>HSCHR17_3_CTG4</div><div>HSCHR17_4_CTG4</div><div>HSCHR17_5_CTG4</div><div>HSCHR17_6_CTG4</div><div>HSCHR18_1_CTG1_1</div>
<div>HSCHR18_1_CTG2_1</div><div>HSCHR18_2_CTG2</div><div>HSCHR18_2_CTG2_1</div><div>HSCHR19_1_CTG3</div><div>HSCHR19_1_CTG3_1</div><div>HSCHR19_2_CTG3</div><div>HSCHR19_3_CTG3</div><div>HSCHR19LRC_COX1_CTG1</div><div>HSCHR19LRC_COX2_CTG1</div>
<div>HSCHR19LRC_LRC_I_CTG1</div><div>HSCHR19LRC_LRC_J_CTG1</div><div>HSCHR19LRC_LRC_S_CTG1</div><div>HSCHR19LRC_LRC_T_CTG1</div><div>HSCHR19LRC_PGF1_CTG1</div><div>HSCHR19LRC_PGF2_CTG1</div><div>HSCHR20_1_CTG1</div><div>
HSCHR21_2_CTG1_1</div>
<div>HSCHR21_3_CTG1_1</div><div>HSCHR21_4_CTG1_1</div><div>HSCHR2_1_CTG1</div><div>HSCHR2_1_CTG12</div><div>HSCHR22_1_CTG1</div><div>HSCHR22_1_CTG2</div><div>HSCHR22_2_CTG1</div><div>HSCHR2_2_CTG12</div><div>HSCHR3_1_CTG1</div>
<div>HSCHR3_1_CTG2_1</div><div>HSCHR4_1</div><div>HSCHR4_1_CTG12</div><div>HSCHR4_1_CTG6</div><div>HSCHR4_2_CTG9</div><div>HSCHR5_1_CTG1</div><div>HSCHR5_1_CTG2</div><div>HSCHR5_1_CTG5</div><div>HSCHR5_2_CTG1</div><div>HSCHR5_3_CTG1</div>
<div>HSCHR6_1_CTG5</div><div>HSCHR6_MHC_APD</div><div>HSCHR6_MHC_COX</div><div>HSCHR6_MHC_DBB</div><div>HSCHR6_MHC_MANN</div><div>HSCHR6_MHC_MCF</div><div>HSCHR6_MHC_QBL</div><div>HSCHR6_MHC_SSTO</div><div>HSCHR7_1_CTG6</div>
<div>HSCHR9_1_CTG1</div><div>HSCHR9_1_CTG35</div><div>HSCHR9_2_CTG35</div><div>HSCHR9_3_CTG35</div><div>MT</div><div>X</div><div>Y</div><div><br></div></div></div><div class="gmail_extra"><div><div class="h5"><br><br><div class="gmail_quote">
On 24 March 2014 07:58, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Enrico,<br>
<br>
HG883_PATCH is indeed a patch.<br>
The human reference assembly contains fix patches, which attempt to correct sequencing errors in the primary assembly, as well as novel patches, or haplotypes.<br>
More information here:<br>
<a href="http://www.ensembl.org/Help/Glossary?id=297" target="_blank">http://www.ensembl.org/Help/<u></u>Glossary?id=297</a><br>
<br>
HG883_PATCH is located on chromosome 17, as can be seen on this view:<br>
<a href="http://www.ensembl.org/Homo_sapiens/Location/View?db=core;r=HG883_PATCH:26729129-26731068" target="_blank">http://www.ensembl.org/Homo_<u></u>sapiens/Location/View?db=core;<u></u>r=HG883_PATCH:26729129-<u></u>26731068</a><br>
If you click outside of the green region, it will tell you which chromosome you are on.<br>
<br>
LRGs are Locus Reference Genomic.<br>
These provide an assembly-independent gene location and are mainly used by the diagnostic community.<br>
More information here:<br>
<a href="http://www.ensembl.org/Help/Glossary?id=406" target="_blank">http://www.ensembl.org/Help/<u></u>Glossary?id=406</a><br>
<br>
To ensure the uniqueness of a sequence, you should align it against the primary assembly, hence excluding all alternative sequences.<br>
On our ftp site (<a href="ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna" target="_blank">ftp://ftp.ensembl.org/pub/<u></u>release-75/fasta/homo_sapiens/<u></u>dna</a>), the sequence is called Homo_sapiens.GRCh37.75.dna_sm.<u></u>primary_assembly.fa<br>
<br>
<br>
Hope that helps,<br>
Magali<div><div><br>
<br>
On 24/03/2014 05:33, Enrico Rubagotti wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
I wish to ensure the uniqueness of ENST00000003834 in the human genome.<br>
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.<br>
HG883_PATCH looks like a patch of the human genome, to which chromosome it refers?<br>
What is LRG_183?<br>
<br>
Please find below the result from blast<br>
<br>
Query= ENSG00000004139|<u></u>ENST00000003834|26691378|<u></u>26728065|17<br>
Length=2916<br>
Score E<br>
Sequences producing significant alignments: (Bits) Value<br>
<br>
ENSG00000004139|<u></u>ENST00000003834|26691378|<u></u>26728065|17 5385 0.0<br>
LRG_183|LRG_183t1|5001|16567|<u></u>LRG_183 3701 0.0<br>
ENSG00000076351|<u></u>ENST00000583295|26721661|<u></u>26734215|17 3701 0.0<br>
ENSG00000076351|<u></u>ENST00000584729|26721661|<u></u>26734215|17 3701 0.0<br>
ENSG00000267556|<u></u>ENST00000591663|26691378|<u></u>26725182|HG883_PATCH 1615 0.0<br>
ENSG00000267556|<u></u>ENST00000585482|26691378|<u></u>26725182|HG883_PATCH 1242 0.0<br>
ENSG00000004139|<u></u>ENST00000578128|26691378|<u></u>26728065|17 1242 0.0<br>
ENSG00000004139|<u></u>ENST00000579593|26691378|<u></u>26728065|17 1227 0.0<br>
ENSG00000267556|<u></u>ENST00000585569|26691378|<u></u>26725182|HG883_PATCH 660 0.0<br>
ENSG00000004139|<u></u>ENST00000577870|26691378|<u></u>26728065|17 660 0.0<br>
ENSG00000267556|<u></u>ENST00000589014|26691378|<u></u>26725182|HG883_PATCH 278 2e-72<br>
ENSG00000004139|<u></u>ENST00000582323|26691378|<u></u>26728065|17 278 2e-72<br>
ENSG00000267556|<u></u>ENST00000591907|26691378|<u></u>26725182|HG883_PATCH 154 3e-35<br>
<br>
Kind regards,<br>
<br>
Enrico<br>
<br>
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</blockquote>
<br>
<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div></div></div><span class="HOEnZb"><font color="#888888">-- <br><div dir="ltr">G.</div>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">G.</div>
</div>