Name
Abstract | ||
|---|---|---|
Methods for the clustering of genes into homologous families (sets of genes descending from a single gene in an ancestral organism) are susceptible to the inappropriate merging of unrelated families, called domain chaining. We give formal criteria for the chaining effect by defining multiple alternative clique relaxation and path relaxation models and the relationships among them, involving different graph characteristics. We implement these definitions and apply them to 45 flowering plant genomes in order to compare the Markov Cluster Algorithm (MCL) and Soft Cliques with Backbones (SCWiB) clustering method. In the process we note the extreme behavior of the Amborella trichopoda genome. |
Year | DOI | Venue |
|---|---|---|
2015 | 10.1007/978-3-662-48221-6_22 | ALGORITHMS IN BIOINFORMATICS (WABI 2015) |
Field | DocType | Volume |
Genome,Forward chaining,Graph,Chaining,Combinatorics,Clique,Computer science,Markov chain,Theoretical computer science,Merge (version control),Cluster analysis | Conference | 9289 |
ISSN | Citations | PageRank |
0302-9743 | 0 | 0.34 |
References | Authors | |
3 | 4 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Poly H. da Silva | 1 | 16 | 1.66 |
| Simone Dantas | 2 | 119 | 24.99 |
| Chunfang Zheng | 3 | 357 | 28.83 |
| David Sankoff | 4 | 1590 | 240.76 |