http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=CI12&feed=atom&action=history
CI12 - História úprav
2024-03-29T06:34:34Z
História úprav pre túto stránku na wiki
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http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=CI12&diff=3060&oldid=prev
Brona na 08:03, 14. december 2023
2023-12-14T08:03:17Z
<p></p>
<table class='diff diff-contentalign-left'>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 08:03, 14. december 2023</td>
</tr><tr><td colspan="2" class="diff-lineno">Riadok 34:</td>
<td colspan="2" class="diff-lineno">Riadok 34:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Chceme minimalizovat <math>\sum_{i=1}^n x_i\,</math></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Chceme minimalizovat <math>\sum_{i=1}^n x_i\,</math></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* za podmienky, ze pre kazde j z {1..m} plati <math>\sum_{i:j\in S_i} x_j \ge 1</math></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* za podmienky, ze pre kazde j z {1..m} plati <math>\sum_{i:j\in S_i} x_j \ge 1</math></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">===Zarovnanie sekvencií RNA so štruktúrou===</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Máme dané dve sekvencie RNA a pre každú z nich máme daný zoznam párov báz (pozícií v rámci sekvencie), ktoré by mohli byť prítomné v sekundárnej štruktúre.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">* Zoznam párov môže byť konkrétna známa sekundárna štruktúra danej sekvencie alebo väčšia množina párov, ktoré by sa v štruktúre mohli vyskytovať, napríklad dvojice, ktoré majú pomerne veľkú pravdepodobnosť byť spárené v SCFG modeli alebo dokonca všetky dvojice komplementárnych báz.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Cieľom je nájsť optimálne zarovnanie týchto dvoch sekvencií, v ktorom použijeme obvyklé skórovanie zhôd, nezhôd a medzier, ale navyše pridáme nejaké skóre za zhody v štruktúre. Dva potenciálne páry, každý z jednej sekvencie, považujeme za zarovnané, ak sú navzájom zarovnané bázy na ich obidvoch koncoch. Do skórovania vyberieme podmnožinu zarovnaných párov tak, aby každá báza bola v najviac jednom páre a každému takému páru priradíme nejaké kladné skóre.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-271</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2" class="diff-lineno">Riadok 70:</td>
<td colspan="2" class="diff-lineno">Riadok 61:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Zdroj:</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Zdroj:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Jinbo Xu, Ming Li, Dongsup Kim, and Ying Xu. "RAPTOR: optimal protein threading by linear programming." Journal of bioinformatics and computational biology 1, no. 01 (2003): 95-117. [http://ttic.uchicago.edu/~jinbo/SelectedPubs/RAPTOR.pdf]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Jinbo Xu, Ming Li, Dongsup Kim, and Ying Xu. "RAPTOR: optimal protein threading by linear programming." Journal of bioinformatics and computational biology 1, no. 01 (2003): 95-117. [http://ttic.uchicago.edu/~jinbo/SelectedPubs/RAPTOR.pdf]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">===Iný príklad: Zarovnanie sekvencií RNA so štruktúrou===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Máme dané dve sekvencie RNA a pre každú z nich máme daný zoznam párov báz (pozícií v rámci sekvencie), ktoré by mohli byť prítomné v sekundárnej štruktúre.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* Zoznam párov môže byť konkrétna známa sekundárna štruktúra danej sekvencie alebo väčšia množina párov, ktoré by sa v štruktúre mohli vyskytovať, napríklad dvojice, ktoré majú pomerne veľkú pravdepodobnosť byť spárené v SCFG modeli alebo dokonca všetky dvojice komplementárnych báz.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Cieľom je nájsť optimálne zarovnanie týchto dvoch sekvencií, v ktorom použijeme obvyklé skórovanie zhôd, nezhôd a medzier, ale navyše pridáme nejaké skóre za zhody v štruktúre. Dva potenciálne páry, každý z jednej sekvencie, považujeme za zarovnané, ak sú navzájom zarovnané bázy na ich obidvoch koncoch. Do skórovania vyberieme podmnožinu zarovnaných párov tak, aby každá báza bola v najviac jednom páre a každému takému páru priradíme nejaké kladné skóre.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Detaily:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-271</ins></div></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=CI12&diff=3053&oldid=prev
Brona: /* Protein threading */
2023-12-07T14:22:55Z
<p><span dir="auto"><span class="autocomment">Protein threading</span></span></p>
<table class='diff diff-contentalign-left'>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 14:22, 7. december 2023</td>
</tr><tr><td colspan="2" class="diff-lineno">Riadok 34:</td>
<td colspan="2" class="diff-lineno">Riadok 34:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Chceme minimalizovat <math>\sum_{i=1}^n x_i\,</math></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Chceme minimalizovat <math>\sum_{i=1}^n x_i\,</math></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* za podmienky, ze pre kazde j z {1..m} plati <math>\sum_{i:j\in S_i} x_j \ge 1</math></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* za podmienky, ze pre kazde j z {1..m} plati <math>\sum_{i:j\in S_i} x_j \ge 1</math></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">===Zarovnanie sekvencií RNA so štruktúrou===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Máme dané dve sekvencie RNA a pre každú z nich máme daný zoznam párov báz (pozícií v rámci sekvencie), ktoré by mohli byť prítomné v sekundárnej štruktúre.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* Zoznam párov môže byť konkrétna známa sekundárna štruktúra danej sekvencie alebo väčšia množina párov, ktoré by sa v štruktúre mohli vyskytovať, napríklad dvojice, ktoré majú pomerne veľkú pravdepodobnosť byť spárené v SCFG modeli alebo dokonca všetky dvojice komplementárnych báz.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Cieľom je nájsť optimálne zarovnanie týchto dvoch sekvencií, v ktorom použijeme obvyklé skórovanie zhôd, nezhôd a medzier, ale navyše pridáme nejaké skóre za zhody v štruktúre. Dva potenciálne páry, každý z jednej sekvencie, považujeme za zarovnané, ak sú navzájom zarovnané bázy na ich obidvoch koncoch. Do skórovania vyberieme podmnožinu zarovnaných párov tak, aby každá báza bola v najviac jednom páre a každému takému páru priradíme nejaké kladné skóre.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-271</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>===Protein threading===</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>===Protein threading===</div></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=CI12&diff=2517&oldid=prev
Brona: /* ILP */
2020-12-10T11:10:54Z
<p><span dir="auto"><span class="autocomment">ILP</span></span></p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 11:10, 10. december 2020</td>
</tr><tr><td colspan="2" class="diff-lineno">Riadok 13:</td>
<td colspan="2" class="diff-lineno">Riadok 13:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>===ILP===</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>===ILP===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''<del class="diffchange diffchange-inline">Linearny </del>program:'''  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''<ins class="diffchange diffchange-inline">Lineárny </ins>program:'''  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Mame <del class="diffchange diffchange-inline">realne premenne </del>x_1...x_n, minimalizujeme nejaku ich linearnu kombinaciu <math>\sum_i a_i x_i\,</math> kde a_i su dane vahy.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Mame <ins class="diffchange diffchange-inline">reálne premenné </ins>x_1...x_n, minimalizujeme nejaku ich linearnu kombinaciu <math>\sum_i a_i x_i\,</math> kde a_i su dane vahy.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Mame tiez niekolko podmienok v tvare linearnych rovnosti alebo nerovnosti, napr. <math>\sum_i b_i x_i \le c</math></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Mame tiez niekolko podmienok v tvare linearnych rovnosti alebo nerovnosti, napr. <math>\sum_i b_i x_i \le c</math></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Hladame teda hodnoty premennych, ktore minimalizuju cielovu sumu, ale pre ktore platia vsetky podmienky</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Hladame teda hodnoty premennych, ktore minimalizuju cielovu sumu, ale pre ktore platia vsetky podmienky</div></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=CI12&diff=2516&oldid=prev
Brona: /* Prakticke programy na NP tazke problemy */
2020-12-10T11:05:39Z
<p><span dir="auto"><span class="autocomment">Prakticke programy na NP tazke problemy</span></span></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Staršia verzia</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Verzia zo dňa a času 11:05, 10. december 2020</td>
</tr><tr><td colspan="2" class="diff-lineno">Riadok 1:</td>
<td colspan="2" class="diff-lineno">Riadok 1:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Protein threading==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Protein threading==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>===<del class="diffchange diffchange-inline">Prakticke </del>programy na NP <del class="diffchange diffchange-inline">tazke problemy</del>===</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>===<ins class="diffchange diffchange-inline">Praktické </ins>programy na NP <ins class="diffchange diffchange-inline">ťažké problémy</ins>===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Obcas chceme najst optimalne riesenie nejakeho NP-tazkeho problemu</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Obcas chceme najst optimalne riesenie nejakeho NP-tazkeho problemu</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Jedna moznost je previest na iny NP tazky problem, pre ktory existuju pomerne dobre prakticke programy, napriklad '''integer linear programming (ILP)'''</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Jedna moznost je previest na iny NP tazky problem, pre ktory existuju pomerne dobre prakticke programy, napriklad '''integer linear programming (ILP)'''</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Riadok 8:</td>
<td colspan="2" class="diff-lineno">Riadok 8:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* SCIP [http://scip.zib.de/] nekomercny program pre ILP</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* SCIP [http://scip.zib.de/] nekomercny program pre ILP</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* SYMPHONY v projekte COIN-OR [https://projects.coin-or.org/SYMPHONY]  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* SYMPHONY v projekte COIN-OR [https://projects.coin-or.org/SYMPHONY]  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Minisat [http://minisat.se/] open source SAT solver</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Minisat [http://minisat.se/] open source SAT solver<ins class="diffchange diffchange-inline">, tiež Lingeling, glucose, CryptoMiniSat, painless</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Concorde TSP solver [http://www.tsp.gatech.edu/concorde.html] - riesi problem obchodneho cestujuceho so symetrickymi vzdialenostami, zadarmo na akademicke ucely</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Concorde TSP solver [http://www.tsp.gatech.edu/concorde.html] - riesi problem obchodneho cestujuceho so symetrickymi vzdialenostami, zadarmo na akademicke ucely</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>** Pre zaujimavost: TSP art [http://www.oberlin.edu/math/faculty/bosch/tspart-page.html]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>** Pre zaujimavost: TSP art [http://www.oberlin.edu/math/faculty/bosch/tspart-page.html]</div></td></tr>
</table>
Brona
http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=CI12&diff=2514&oldid=prev
Brona: Vytvorená stránka „==Protein threading== ===Prakticke programy na NP tazke problemy=== * Obcas chceme najst optimalne riesenie nejakeho NP-tazkeho problemu * Jedna moznost je previest na i...“
2020-12-10T10:50:40Z
<p>Vytvorená stránka „==Protein threading== ===Prakticke programy na NP tazke problemy=== * Obcas chceme najst optimalne riesenie nejakeho NP-tazkeho problemu * Jedna moznost je previest na i...“</p>
<p><b>Nová stránka</b></p><div>==Protein threading==<br />
===Prakticke programy na NP tazke problemy===<br />
* Obcas chceme najst optimalne riesenie nejakeho NP-tazkeho problemu<br />
* Jedna moznost je previest na iny NP tazky problem, pre ktory existuju pomerne dobre prakticke programy, napriklad '''integer linear programming (ILP)'''<br />
<br />
* najdu optimalne riesenie, mnohe instancie zrataju v rozumnom case, ale mozu bezat aj velmi dlho<br />
* CPLEX [http://www-01.ibm.com/software/integration/optimization/cplex-optimizer/] a Gurobi [http://www.gurobi.com/html/academic.html] komercne baliky na ILP, akademicka licencia zadarmo<br />
* SCIP [http://scip.zib.de/] nekomercny program pre ILP<br />
* SYMPHONY v projekte COIN-OR [https://projects.coin-or.org/SYMPHONY] <br />
* Minisat [http://minisat.se/] open source SAT solver<br />
* Concorde TSP solver [http://www.tsp.gatech.edu/concorde.html] - riesi problem obchodneho cestujuceho so symetrickymi vzdialenostami, zadarmo na akademicke ucely<br />
** Pre zaujimavost: TSP art [http://www.oberlin.edu/math/faculty/bosch/tspart-page.html]<br />
<br />
===ILP===<br />
'''Linearny program:''' <br />
* Mame realne premenne x_1...x_n, minimalizujeme nejaku ich linearnu kombinaciu <math>\sum_i a_i x_i\,</math> kde a_i su dane vahy.<br />
* Mame tiez niekolko podmienok v tvare linearnych rovnosti alebo nerovnosti, napr. <math>\sum_i b_i x_i \le c</math><br />
* Hladame teda hodnoty premennych, ktore minimalizuju cielovu sumu, ale pre ktore platia vsetky podmienky<br />
* Da sa riesit v polynomialnom case <br />
'''Integer linear program'''<br />
* Program, v ktorom vsetky/vybrane premenne musia mat celociselne hodnoty, alebo dokonca povolime iba hodnoty 0 a 1.<br />
* NP uplny problem<br />
<br />
===Ako zapisat (NP-tazke) problemy ako ILP===<br />
Knapsack<br />
* Problem: mame dane predmety s hmotnostami w_1..w_n a cenami c_1..c_n, ktore z nich vybrat, aby celkova hmotnost bola najviac T a cena bola co najvyssia?<br />
* Pouzijeme binarne premenne x_1..x_n, kde x_i = 1 prave vtedy ked sme zobrali i-ty predmet.<br />
* Chceme maximalizovat <math>\sum_i c_i x_i\,</math><br />
* za podmienky ze <math>\sum_i w_i x_i \le T</math><br />
<br />
Set cover:<br />
* Mame n mnozin S_1...S_n nad mnozinou {1...m}. Chceme vybrat co najmensi pocet zo vstupnych mnozin tak, aby ich zjednotenie bola cela mnozina {1..m}<br />
* Binarne premenne x_i=1 ak vyberieme i-tu mnozinu<br />
* Chceme minimalizovat <math>\sum_{i=1}^n x_i\,</math><br />
* za podmienky, ze pre kazde j z {1..m} plati <math>\sum_{i:j\in S_i} x_j \ge 1</math><br />
<br />
===Protein threading===<br />
* Ciel: protein A ma znamu sekvenciu aj strukturu, protein B iba sekvenciu. Chceme zarovnat proteiny A a B, pricom budeme brat do uvahy znamu strukturu, t.j. ak su dve amino kyseliny blizko v A tak ich ekvivalenty v B by mali byt "kompatibilne". <br />
* Tento problem chceme riesit tak, ze v strukture A urcime nejake jadra, ktore by v evolucii mali zostat zachovane bez inzercii a delecii a v rovnakom poradi. Tieto jadra su oddelene sluckami, ktorych dlzka sa moze lubovolne menit a ktorych zarovnania nebudeme skorovat.<br />
* Formulacia problemu: Mame danu sekvenciu B=b1..bn, dlzky m jadier c_1...c_m a skorovacie tabulky E_ij, ktora vyjadruje, ako dobre bj..b_{j+c_i-1} sedi do sekvencie jadra i a E_ijkl ktora vyjadruje, ako dobre by jadra i a k interagovali, keby mali sekvencie zacinajuce v B na poziciach j a l. Uloha je zvolit polohy jadier x_1<x_2<...<x_m tak, aby sa ziadne dve jadra neprekryvali a aby sme dosiahli najvyssie skore.<br />
* Poznamka: nevraveli sme, ako konkretne zvolit jadra a skorovacie tabulky, co je modelovaci, nie algoritmicky problem (mozeme skusit napr. nejake pravdepodobnostne modely)<br />
<br />
===Protein threading ako ILP===<br />
* Premenne v programe: <br />
** x_ij=1 ak je zaciatok i-teho jadra zarovnane s b_j<br />
** y_ijkl=1 ak je zaciatok i-teho jadra na b_j a zaciatok k-teho na b_l (i<k, j<l)<br />
* Chceme maximalizovat <math>\sum E_{ij} x_{ij} + \sum E_{ijkl} y_{ijkl}</math><br />
* Podmienky:<br />
** <math>\sum_j x_{ij}=1\,</math> pre kazde i<br />
** <math>x_{il}+x_{i+1,k}\le 1</math> pre vsetky i,k,l, kde k<l+c_i<br />
** <math>y_{ijkl}\le x_{ij}</math> pre vsetky i,j,k,l, kde i<k, j<l<br />
** <math>y_{ijkl}\le x_{kl}</math> pre vsetky i,j,k,l, kde i<k, j<l<br />
** <math>y_{ijkl}\ge x_{ij}+x_{kl}-1</math> pre vsetky i,j,k,l, kde i<k, j<l<br />
<br />
Na zamyslenie:<br />
* Aka bude velkost programu ako funkcia n a m?<br />
* Co ak nie vsetky jadra navzajom interaguju? Mozeme na velkosti programu usetrit?<br />
* Preco asi vobec autori zaviedli jadra a ako by sme zmenili program, ak by sme chceli uvazovat kazdu aminokyselinu zvlast?<br />
<br />
Zdroj:<br />
* Jinbo Xu, Ming Li, Dongsup Kim, and Ying Xu. "RAPTOR: optimal protein threading by linear programming." Journal of bioinformatics and computational biology 1, no. 01 (2003): 95-117. [http://ttic.uchicago.edu/~jinbo/SelectedPubs/RAPTOR.pdf]</div>
Brona