AlignNemo

[…] to-many mappings. However, local aligners focus on the most conserved regions of the networks, and thus return very small alignments. Although local aligners are not designed to align large networks (AlignNemo, AlignMCL and LocalAli all encounter memory issues on our datasets), we were able to use AlignNemo to align our smallest pair of networks, R. norvegicus PPI network (1,657 nodes and 2,330 ed […]

[…] in pair in a single network is unequal with respect to the difference of input PPI networks, which is determined by inputting parameters l and r. For example, when taking the same lenient criteria as AlignNemo and DAMAlign do, UEDAMAlign absorbs a pair of homologous proteins into its predicted conserved protein complexes if at least one of protein in the homologous protein pair connects to the pro […]

[…] t is based on Markov clustering (MCL), a known graph clustering algorithm that simulates random walks using Markov chains iteratively. AlignMCL first builds a weighted alignment graph the same way as AlignNemo. Next, it applies MCL to this graph to identify conserved protein modules. Graemlin 1.0 [] is an early multiple aligner. Based on a phylogenetic tree of species whose networks are being alig […]

[…] For the SceDIP and SceBGS networks, we report the performance of ASModel, NCut, MCL, RMCL, and AlignNemo on complex prediction in terms of the number of matched reference complexes and F-measure. The detailed information such as the number of clusters (cluster size ≥ 2) and the coverage is list […]