Sentence examples for uses the mcl algorithm from inspiring English sources

This version of OrthologID uses the MCL algorithm [ 54, 55] for improved clustering and includes automated extraction of orthologs from gene trees into a partitioned matrix.

The line graph generation approach [ 9] transforms the network of proteins connected by interactions into a network of connected interactions and then uses the MCL algorithm to cluster the interaction network.

The network was clustered into groups of genes sharing similar profiles using the MCL algorithm with an empirical MCL inflation value (1.8) and a global graph for each network was created showing the MCL clusters.

This can be attributed to the nature of the IMG ortholog clustering that divides proteins with bidirectional best hits using the MCL algorithm, thus resulting in many more clusters of finer granularity.

We grouped the proteins based on their subcellular location and clustered them using the MCL algorithm in order to detect functional modules.

We combined BLAST-based selection of clusters using the MCL algorithm with further automated phylogenetic screening of families and paralogs (see Materials and Methods).

Clustering into protein families using the MCL algorithm yielded 2413 shared protein families with 3385 and 3187 members in Synechocystis 6803 and 6714, respectively.

Protein-Protein Interactions (PPIs) for a particular species e.g. yeast, were combined into a Protein Interaction Network (PIN) and clustered using the MCL algorithm (see methods).

Their orthology relationships were assessed by using the MCL algorithm (Enright et al. 2002) and further inspection of within-group multiple alignments and pairwise Smith Waterman alignments as implemented by EMBOSS (Rice et al. 2000).

However, many of the strain-specific genes belong to gene families that were clustered as paralogues to pairs of orthologue genes when using the MCL algorithm, indicating gene duplications, sequence, and probably also functional diversification.

In addition to improved execution pipeline on Sun Grid Engine clusters, this version of OrthologID used the MCL algorithm (Enright et al. 2002; Van Dongen 2008) for improved clustering and included automated extraction of orthologs from gene trees into a partitioned matrix in a single package.