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research [2020/02/28 13:41]
tischulz Updated links
research [2020/02/28 13:54] (current)
tischulz Added graph teams software
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 === Detection of Gene Clusters === === Detection of Gene Clusters ===
  
-{{:​zellen.png?​nolink |Zellen|}}Gene clusters are sets of genetic markers that maintain close physical proximities to each other in several genomes. These genetic markers often embody protein coding genes that are functionally and/or regulatorily associated.\\ Traditional methods take into account one-dimensional distances in the genomic sequence to determine physical proximities. They do not consider any spatial information regarding the structure of the chromatid in the cell and therefore might miss spatial gene clusters within the genome. However, spatial structure and function seem to be correlated in many cases.\\ Nowadays, it is possible to gain three-dimensional information about the chromatid in the cell (e.g. by Hi-C experiments).\\ We try to include this Hi-C data to improve the gene cluster model in a spatial manner ​which on the other hand - seems to raise the computational complexity. The aim is to develop ​a polynomial algorithm that is able to find all common spatial gene clusters between two genomes.+{{:​zellen.png?​nolink |Zellen|}}Gene clusters are sets of genetic markers that maintain close physical proximities to each other in several genomes. These genetic markers often embody protein coding genes that are functionally and/or regulatorily associated.\\ Traditional methods take into account one-dimensional distances in the genomic sequence to determine physical proximities. They do not consider any spatial information regarding the structure of the chromatid in the cell and therefore might miss spatial gene clusters within the genome. However, spatial structure and function seem to be correlated in many cases.\\ Nowadays, it is possible to gain three-dimensional information about the chromatid in the cell (e.g. by Hi-C experiments).\\ We try to include this Hi-C data to improve the gene cluster model in a spatial manner. With [[https://​bibiserv.cebitec.uni-bielefeld.de/​graphteams|GraphTeams]],​ we presented ​the the first gene cluster model capable of handling spatial data. The program implements ​a polynomial ​time algorithm that is able to find all common spatial gene clusters between two genomes.
  
 === Evolution of Gene Clusters === === Evolution of Gene Clusters ===