Difference between revisions of "Protocol-msud-task5 protocol"

From Bioinformatikpedia
(→‎HGMD)
(→‎SNPdbe)
Line 34: Line 34:
   
 
= SNPdbe =
  
= SNPdbe =
−  
 
<table border=1>
  
<table border=1>
−
<tr><td>Mutation </td><td> Experimental evidence </td></tr>
 +
<tr><td>Mutation </td><td> Experimental evidence </td><td> Pssm wt </td></tr>
−
<tr><td>V3G</td><td>Not validated</td></tr>
 +
<tr><td>V3G</td><td>Not validated</td><td>69</td></tr>
−
<tr><td>L17F</td><td>Not validated</td></tr>
 +
<tr><td>L17F</td><td>Not validated</td><td>29</td></tr>
−
<tr><td>L17F</td><td>Not validated</td></tr>
 +
<tr><td>L17F</td><td>Not validated</td><td>31</td></tr>
−
<tr><td>G29E</td><td>Not validated</td></tr>
 +
<tr><td>G29E</td><td>Not validated</td><td>34</td></tr>
−
<tr><td>G29E</td><td>Not validated</td></tr>
 +
<tr><td>G29E</td><td>Not validated</td><td>27</td></tr>
−
<tr><td>S36A</td><td>Not validated</td></tr>
 +
<tr><td>S36A</td><td>Not validated</td><td>36</td></tr>
−
<tr><td>P39H</td><td>Not validated</td></tr>
 +
<tr><td>P39H</td><td>Not validated</td><td>42</td></tr>
−
<tr><td>P39H</td><td>Not validated</td></tr>
 +
<tr><td>P39H</td><td>Not validated</td><td>40</td></tr>
−
<tr><td>Q42R</td><td>Not validated</td></tr>
 +
<tr><td>Q42R</td><td>Not validated</td><td>23</td></tr>
−
<tr><td>Q42R</td><td>Not validated</td></tr>
 +
<tr><td>Q42R</td><td>Not validated</td><td>26</td></tr>
−
<tr><td>A59V</td><td>Not validated</td></tr>
 +
<tr><td>A59V</td><td>Not validated</td><td>30</td></tr>
−
<tr><td>A59V</td><td>Not validated</td></tr>
 +
<tr><td>A59V</td><td>Not validated</td><td>32</td></tr>
−
<tr><td>I62M</td><td>Not validated</td></tr>
 +
<tr><td>I62M</td><td>Not validated</td><td>8</td></tr>
−
<tr><td>I62M</td><td>Not validated</td></tr>
 +
<tr><td>I62M</td><td>Not validated</td><td>7</td></tr>
−
<tr><td>N71S</td><td>Not validated</td></tr>
 +
<tr><td>N71S</td><td>Not validated</td><td>12</td></tr>
−
<tr><td>N71S</td><td>Not validated</td></tr>
 +
<tr><td>N71S</td><td>Not validated</td><td>12</td></tr>
−
<tr><td>M82I</td><td>Not validated</td></tr>
 +
<tr><td>M82I</td><td>Not validated</td><td>10</td></tr>
−
<tr><td>M82L</td><td>Not validated</td></tr>
 +
<tr><td>M82L</td><td>Not validated</td><td>10</td></tr>
−
<tr><td>M82I</td><td>Not validated</td></tr>
 +
<tr><td>M82I</td><td>Not validated</td><td>11</td></tr>
−
<tr><td>M82L</td><td>Not validated</td></tr>
 +
<tr><td>M82L</td><td>Not validated</td><td>10</td></tr>
−
<tr><td>R117C</td><td>Not validated</td></tr>
 +
<tr><td>R117C</td><td>Not validated</td><td>6</td></tr>
−
<tr><td>R117C</td><td>Not validated</td></tr>
 +
<tr><td>R117C</td><td>Not validated</td><td>6</td></tr>
−
<tr><td>R127W</td><td>Not validated</td></tr>
 +
<tr><td>R127W</td><td>Not validated</td><td>23</td></tr>
−
<tr><td>R127W</td><td>Not validated</td></tr>
 +
<tr><td>R127W</td><td>Not validated</td><td>21</td></tr>
−
<tr><td>N150D</td><td>Not validated</td></tr>
 +
<tr><td>N150D</td><td>Not validated</td><td>4</td></tr>
−
<tr><td>N150D</td><td>Not validated</td></tr>
 +
<tr><td>N150D</td><td>Not validated</td><td>4</td></tr>
−
<tr><td>T151M</td><td>Not validated</td></tr>
 +
<tr><td>T151M</td><td>Not validated</td><td>7</td></tr>
−
<tr><td>T151M</td><td>Not validated</td></tr>
 +
<tr><td>T151M</td><td>Not validated</td><td>7</td></tr>
−
<tr><td>Q157A</td><td>Not validated</td></tr>
 +
<tr><td>Q157A</td><td>Not validated</td><td>5</td></tr>
−
<tr><td>Y158A</td><td>Not validated</td></tr>
 +
<tr><td>Y158A</td><td>Not validated</td><td>6</td></tr>
−
<tr><td>R159W</td><td>Not validated</td></tr>
 +
<tr><td>R159W</td><td>Not validated</td><td>65</td></tr>
−
<tr><td>R159A</td><td>Not validated</td></tr>
 +
<tr><td>R159A</td><td>Not validated</td><td>65</td></tr>
−
<tr><td>P170S</td><td>Not validated</td></tr>
 +
<tr><td>P170S</td><td>Not validated</td><td>24</td></tr>
−
<tr><td>P170S</td><td>Not validated</td></tr>
 +
<tr><td>P170S</td><td>Not validated</td><td>24</td></tr>
−
<tr><td>Q190K</td><td>Not validated</td></tr>
 +
<tr><td>Q190K</td><td>Not validated</td><td>19</td></tr>
−
<tr><td>R200C</td><td>Not validated</td></tr>
 +
<tr><td>R200C</td><td>Not validated</td><td>6</td></tr>
−
<tr><td>R200C</td><td>Not validated</td></tr>
 +
<tr><td>R200C</td><td>Not validated</td><td>6</td></tr>
−
<tr><td>S207A</td><td>Not validated</td></tr>
 +
<tr><td>S207A</td><td>Not validated</td><td>12</td></tr>
−
<tr><td>L209A</td><td>Not validated</td></tr>
 +
<tr><td>L209A</td><td>Not validated</td><td>6</td></tr>
−
<tr><td>T211A</td><td>Not validated</td></tr>
 +
<tr><td>T211A</td><td>Not validated</td><td>13</td></tr>
−
<tr><td>T211M</td><td>Not validated</td></tr>
 +
<tr><td>T211M</td><td>Not validated</td><td>13</td></tr>
−
<tr><td>A222T</td><td>Not validated</td></tr>
 +
<tr><td>A222T</td><td>Not validated</td><td>60</td></tr>
−
<tr><td>A222T</td><td>Not validated</td></tr>
 +
<tr><td>A222T</td><td>Not validated</td><td>60</td></tr>
−
<tr><td>E238A</td><td>Not validated</td></tr>
 +
<tr><td>E238A</td><td>Not validated</td><td>8</td></tr>
−
<tr><td>G244R</td><td>Not validated</td></tr>
 +
<tr><td>G244R</td><td>Not validated</td><td>72</td></tr>
−
<tr><td>G244R</td><td>Not validated</td></tr>
 +
<tr><td>G244R</td><td>Not validated</td><td>71</td></tr>
−
<tr><td>A248D</td><td>Not validated</td></tr>
 +
<tr><td>A248D</td><td>Not validated</td><td>5</td></tr>
−
<tr><td>G249S</td><td>Not validated</td></tr>
 +
<tr><td>G249S</td><td>Not validated</td><td>11</td></tr>
−
<tr><td>G249S</td><td>Not validated</td></tr>
 +
<tr><td>G249S</td><td>Not validated</td><td>11</td></tr>
−
<tr><td>A253T</td><td>Not validated</td></tr>
 +
<tr><td>A253T</td><td>Not validated</td><td>66</td></tr>
−
<tr><td>A253T</td><td>Not validated</td></tr>
 +
<tr><td>A253T</td><td>Not validated</td><td>70</td></tr>
−
<tr><td>A254D</td><td>Not validated</td></tr>
 +
<tr><td>A254D</td><td>Not validated</td><td>21</td></tr>
−
<tr><td>C264W</td><td>Not validated</td></tr>
 +
<tr><td>C264W</td><td>Not validated</td><td>11</td></tr>
−
<tr><td>C264W</td><td>Not validated</td></tr>
 +
<tr><td>C264W</td><td>Not validated</td><td>13</td></tr>
−
<tr><td>R265W</td><td>Not validated</td></tr>
 +
<tr><td>R265W</td><td>Not validated</td><td>6</td></tr>
−
<tr><td>R265W</td><td>Not validated</td></tr>
 +
<tr><td>R265W</td><td>Not validated</td><td>5</td></tr>
−
<tr><td>R265K</td><td>Not validated</td></tr>
 +
<tr><td>R265K</td><td>Not validated</td><td>5</td></tr>
−
<tr><td>R265A</td><td>Not validated</td></tr>
 +
<tr><td>R265A</td><td>Not validated</td><td>5</td></tr>
−
<tr><td>N267S</td><td>Not validated</td></tr>
 +
<tr><td>N267S</td><td>Not validated</td><td>62</td></tr>
−
<tr><td>Y269A</td><td>Not validated</td></tr>
 +
<tr><td>Y269A</td><td>Not validated</td><td>21</td></tr>
−
<tr><td>A285P</td><td>Not validated</td></tr>
 +
<tr><td>A285P</td><td>Not validated</td><td>32</td></tr>
−
<tr><td>G289R</td><td>Not validated</td></tr>
 +
<tr><td>G289R</td><td>Not validated</td><td>25</td></tr>
−
<tr><td>G290R</td><td>Not validated</td></tr>
 +
<tr><td>G290R</td><td>Not validated</td><td>22</td></tr>
−
<tr><td>R296C</td><td>Not validated</td></tr>
 +
<tr><td>R296C</td><td>Not validated</td><td>15</td></tr>
−
<tr><td>R297C</td><td>Not validated</td></tr>
 +
<tr><td>R297C</td><td>Not validated</td><td>17</td></tr>
−
<tr><td>Y306H</td><td>Not validated</td></tr>
 +
<tr><td>Y306H</td><td>Not validated</td><td>12</td></tr>
−
<tr><td>Y307H</td><td>Not validated</td></tr>
 +
<tr><td>Y307H</td><td>Not validated</td><td>12</td></tr>
−
<tr><td>T309R</td><td>Not validated</td></tr>
 +
<tr><td>T309R</td><td>Not validated</td><td>9</td></tr>
−
<tr><td>T310R</td><td>Not validated</td></tr>
 +
<tr><td>T310R</td><td>Not validated</td><td>8</td></tr>
−
<tr><td>R313Q</td><td>Not validated</td></tr>
 +
<tr><td>R313Q</td><td>Not validated</td><td>10</td></tr>
−
<tr><td>R314Q</td><td>Not validated</td></tr>
 +
<tr><td>R314Q</td><td>Not validated</td><td>10</td></tr>
−
<tr><td>I326T</td><td>Not validated</td></tr>
 +
<tr><td>I326T</td><td>Not validated</td><td>26</td></tr>
−
<tr><td>H336A</td><td>Not validated</td></tr>
 +
<tr><td>H336A</td><td>Not validated</td><td>52</td></tr>
−
<tr><td>S337D</td><td>Not validated</td></tr>
 +
<tr><td>S337D</td><td>Not validated</td><td>27</td></tr>
−
<tr><td>A343V</td><td>Not validated</td></tr>
 +
<tr><td>A343V</td><td>Not validated</td><td>17</td></tr>
−
<tr><td>A344V</td><td>Not validated</td></tr>
 +
<tr><td>A344V</td><td>Not validated</td><td>16</td></tr>
−
<tr><td>R345C</td><td>Not validated</td></tr>
 +
<tr><td>R345C</td><td>Not validated</td><td>16</td></tr>
−
<tr><td>S346L</td><td>Not validated</td></tr>
 +
<tr><td>S346L</td><td>Not validated</td><td>5</td></tr>
−
<tr><td>R346C</td><td>Not validated</td></tr>
 +
<tr><td>R346C</td><td>Not validated</td><td>17</td></tr>
−
<tr><td>S347L</td><td>Not validated</td></tr>
 +
<tr><td>S347L</td><td>Not validated</td><td>5</td></tr>
−
<tr><td>W354F</td><td>Not validated</td></tr>
 +
<tr><td>W354F</td><td>Not validated</td><td>30</td></tr>
−
<tr><td>Q356R</td><td>Not validated</td></tr>
 +
<tr><td>Q356R</td><td>Not validated</td><td>7</td></tr>
−
<tr><td>Q357R</td><td>Not validated</td></tr>
 +
<tr><td>Q357R</td><td>Not validated</td><td>7</td></tr>
−
<tr><td>I360V</td><td>Not validated</td></tr>
 +
<tr><td>I360V</td><td>Not validated</td><td>32</td></tr>
−
<tr><td>I361V</td><td>Not validated</td></tr>
 +
<tr><td>I361V</td><td>Not validated</td><td>32</td></tr>
−
<tr><td>E397K</td><td>Not validated</td></tr>
 +
<tr><td>E397K</td><td>Not validated</td><td>26</td></tr>
−
<tr><td>E398K</td><td>Not validated</td></tr>
 +
<tr><td>E398K</td><td>Not validated</td><td>27</td></tr>
−
<tr><td>R398Q</td><td>Not validated</td></tr>
 +
<tr><td>R398Q</td><td>Not validated</td><td>6</td></tr>
−
<tr><td>R399Q</td><td>Not validated</td></tr>
 +
<tr><td>R399Q</td><td>Not validated</td><td>6</td></tr>
−
<tr><td>P402R</td><td>Not validated</td></tr>
 +
<tr><td>P402R</td><td>Not validated</td><td>53</td></tr>
−
<tr><td>P403R</td><td>Not validated</td></tr>
 +
<tr><td>P403R</td><td>Not validated</td><td>53</td></tr>
−
<tr><td>N403S</td><td>Not validated</td></tr>
 +
<tr><td>N403S</td><td>Not validated</td><td>5</td></tr>
−
<tr><td>N404S</td><td>Not validated</td></tr>
 +
<tr><td>N404S</td><td>Not validated</td><td>6</td></tr>
−
<tr><td>F408C</td><td>Not validated</td></tr>
 +
<tr><td>F408C</td><td>Not validated</td><td>40</td></tr>
−
<tr><td>F409C</td><td>Not validated</td></tr>
 +
<tr><td>F409C</td><td>Not validated</td><td>41</td></tr>
−
<tr><td>Y413C</td><td>Not validated</td></tr>
 +
<tr><td>Y413C</td><td>Not validated</td><td>57</td></tr>
−
<tr><td>Q423K</td><td>Not validated</td></tr>
 +
<tr><td>Q423K</td><td>Not validated</td><td>4</td></tr>
−
<tr><td>Q424K</td><td>Not validated</td></tr>
 +
<tr><td>Q424K</td><td>Not validated</td><td>6</td></tr>
−
<tr><td>R428H</td><td>Not validated</td></tr>
 +
<tr><td>R428H</td><td>Not validated</td><td>13</td></tr>
−
<tr><td>R429H</td><td>Not validated</td></tr>
 +
<tr><td>R429H</td><td>Not validated</td><td>14</td></tr>
−
<tr><td>Y437N</td><td>Not validated</td></tr>
 +
<tr><td>Y437N</td><td>Not validated</td><td>51</td></tr>
−
<tr><td>Y438N</td><td>Not validated</td></tr>
 +
<tr><td>Y438N</td><td>Not validated</td><td>53</td></tr>
 
</table>
  
</table>

Revision as of 17:48, 5 June 2012

HGMD

sequence used by HGMD can be found [here] 

>gi|38372929|ref|NM_000709.2| Homo sapiens branched chain keto acid dehydrogenase E1, alpha polypeptide (BCKDHA), mRNA
GCCGGACCGCTGAGTGGTTGTTAGCCAAGATGGCGGTAGCGATCGCTGCAGCGAGGGTCTGGCGGCTAAA
CCGTGGTTTGAGCCAGGCTGCCCTCCTGCTGCTGCGGCAGCCTGGGGCTCGGGGACTGGCTAGATCTCAC
CCCCCCAGGCAGCAGCAGCAGTTTTCATCTCTGGATGACAAGCCCCAGTTCCCAGGGGCCTCGGCGGAGT
TTATAGATAAGTTGGAATTCATCCAGCCCAACGTCATCTCTGGAATCCCCATCTACCGCGTCATGGACCG
GCAAGGCCAGATCATCAACCCCAGCGAGGACCCCCACCTGCCGAAGGAGAAGGTGCTGAAGCTCTACAAG
AGCATGACACTGCTTAACACCATGGACCGCATCCTCTATGAGTCTCAGCGGCAGGGCCGGATCTCCTTCT
ACATGACCAACTATGGTGAGGAGGGCACGCACGTGGGGAGTGCCGCCGCCCTGGACAACACGGACCTGGT
GTTTGGCCAGTACCGGGAGGCAGGTGTGCTGATGTATCGGGACTACCCCCTGGAACTATTCATGGCCCAG
TGCTATGGCAACATCAGTGACTTGGGCAAGGGGCGCCAGATGCCTGTCCACTACGGCTGCAAGGAACGCC
ACTTCGTCACTATCTCCTCTCCACTGGCCACGCAGATCCCTCAGGCGGTGGGGGCGGCGTACGCAGCCAA
GCGGGCCAATGCCAACAGGGTCGTCATCTGTTACTTCGGCGAGGGGGCAGCCAGTGAGGGGGACGCCCAT
GCCGGCTTCAACTTCGCTGCCACACTTGAGTGCCCCATCATCTTCTTCTGCCGGAACAATGGCTACGCCA
TCTCCACGCCCACCTCTGAGCAGTATCGCGGCGATGGCATTGCAGCACGAGGCCCCGGGTATGGCATCAT
GTCAATCCGCGTGGATGGTAATGATGTGTTTGCCGTATACAACGCCACAAAGGAGGCCCGACGGCGGGCT
GTGGCAGAGAACCAGCCCTTCCTCATCGAGGCCATGACCTACAGGATCGGGCACCACAGCACCAGTGACG
ACAGTTCAGCGTACCGCTCGGTGGATGAGGTCAATTACTGGGATAAACAGGACCACCCCATCTCCCGGCT
GCGGCACTATCTGCTGAGCCAAGGCTGGTGGGATGAGGAGCAGGAGAAGGCCTGGAGGAAGCAGTCCCGC
AGGAAGGTGATGGAGGCCTTTGAGCAGGCCGAGCGGAAGCCCAAACCCAACCCCAACCTACTCTTCTCAG
ACGTGTATCAGGAGATGCCCGCCCAGCTCCGCAAGCAGCAGGAGTCTCTGGCCCGCCACCTGCAGACCTA
CGGGGAGCACTACCCACTGGATCACTTCGATAAGTGAGACCTGCTCAGCCCACCCCCACCCATCCTCAGC
TACCCCGAGAGGTAGCCCCACTCTAAGGGGAGCAGGGGGACCTGACAGCACACCACTGTCTTCCCCAGTC
AGCTCCCTCTAAAATACTCAGCGGCCAGGGCGGCTGCCACTCTTCACCCCTGCTCCTCCCGGCTGTTACA
TTGTCAGGGGACAGCATCTGCAGCAGTTGCTGAGGCTCCGTCAGCCCCCTCTTCACCTGTTGTTACAGTG
CCTTCTCCCAGGGGCTGGGTGAGGGCACATTCAGGACTAGAAGCCCCTCTGGGCATGGGGTGGACATGGC
AGGTCAGCCTGTGGAACTTGCGCAGGTGCGAGTGGCCAGCAGAGGTCACGAATAAACTGCATCTCTGCGC
CTGGCTCTCTACCAAAAAAAAAAAAAAAAAA

All Missense/Nonsense mutations listed in HGMD: 

Q125E, T151M, D152N, R159W, Y166N, R167Q, Q190K, I213T, A216V, A220V, G249S, A253T, C258Y, C264W, R265W, N267S, G283D, A285P, 
R287TERM, G290R, R297C, R297H, G300S, D302A, T310R, R314TERM, I326T, E327K, A328T, R346H, R363W, F409C, V412M, Y413H, Y413C, Y438N,

SNPdbe

Mutation Experimental evidence Pssm wt
V3GNot validated69
L17FNot validated29
L17FNot validated31
G29ENot validated34
G29ENot validated27
S36ANot validated36
P39HNot validated42
P39HNot validated40
Q42RNot validated23
Q42RNot validated26
A59VNot validated30
A59VNot validated32
I62MNot validated8
I62MNot validated7
N71SNot validated12
N71SNot validated12
M82INot validated10
M82LNot validated10
M82INot validated11
M82LNot validated10
R117CNot validated6
R117CNot validated6
R127WNot validated23
R127WNot validated21
N150DNot validated4
N150DNot validated4
T151MNot validated7
T151MNot validated7
Q157ANot validated5
Y158ANot validated6
R159WNot validated65
R159ANot validated65
P170SNot validated24
P170SNot validated24
Q190KNot validated19
R200CNot validated6
R200CNot validated6
S207ANot validated12
L209ANot validated6
T211ANot validated13
T211MNot validated13
A222TNot validated60
A222TNot validated60
E238ANot validated8
G244RNot validated72
G244RNot validated71
A248DNot validated5
G249SNot validated11
G249SNot validated11
A253TNot validated66
A253TNot validated70
A254DNot validated21
C264WNot validated11
C264WNot validated13
R265WNot validated6
R265WNot validated5
R265KNot validated5
R265ANot validated5
N267SNot validated62
Y269ANot validated21
A285PNot validated32
G289RNot validated25
G290RNot validated22
R296CNot validated15
R297CNot validated17
Y306HNot validated12
Y307HNot validated12
T309RNot validated9
T310RNot validated8
R313QNot validated10
R314QNot validated10
I326TNot validated26
H336ANot validated52
S337DNot validated27
A343VNot validated17
A344VNot validated16
R345CNot validated16
S346LNot validated5
R346CNot validated17
S347LNot validated5
W354FNot validated30
Q356RNot validated7
Q357RNot validated7
I360VNot validated32
I361VNot validated32
E397KNot validated26
E398KNot validated27
R398QNot validated6
R399QNot validated6
P402RNot validated53
P403RNot validated53
N403SNot validated5
N404SNot validated6
F408CNot validated40
F409CNot validated41
Y413CNot validated57
Q423KNot validated4
Q424KNot validated6
R428HNot validated13
R429HNot validated14
Y437NNot validated51
Y438NNot validated53
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