![]() Hence, WAAFLE will report this contig as a one-species contig explained by species C. In Example 1, genes from species C are able to explain all of the loci reasonably well (with scores exceeding k 1). If all per-locus scores for a pair of species exceed a stringent homology threshold (k 2), then the contig is considered a putative LGT between those species.īoth cases consider contigs with six protein-coding loci (determined from WAAFLE itself or an independent ORF-calling program such as Prodigal). Otherwise, the process is repeated for pairs of species. ![]() If one or more species meet this criterion, then the contig is assigned to the species with the best average score. WAAFLE then looks for a species whose minimum per-locus score exceeds a lenient homology threshold (k 1). More specifically, for each locus in a contig, WAAFLE identifies the best hit to each species in a pangenome database. WAAFLE integrates gene sequence homology and taxonomic provenance to identify metagenomic contigs explained by pairs of microbial clades but not by single clades (i.e.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |