PathRacer swMATH ID: 29679 Software Authors: Shlemov, Alexander; Korobeynikov, Anton Description: PathRacer: racing profile HMM paths on assembly graph. Recently large databases containing profile Hidden Markov Models (pHMMs) emerged. These pHMMs may represent the sequences of antibiotic resistance genes, or allelic variations amongst highly conserved housekeeping genes used for strain typing, etc. The typical application of such a database includes the alignment of contigs to pHMM hoping that the sequence of gene of interest is located within the single contig. Such a condition is often violated for metagenomes preventing the effective use of such databases. We present PathRacer—a novel standalone tool that aligns profile HMM directly to the assembly graph (performing the codon translation on fly for amino acid pHMMs). The tool provides the set of most probable paths traversed by a HMM through the whole assembly graph, regardless whether the sequence of interested is encoded on the single contig or scattered across the set of edges, therefore significantly improving the recovery of sequences of interest even from fragmented metagenome assemblies. Homepage: https://link.springer.com/chapter/10.1007%2F978-3-030-18174-1_6 Keywords: profile HMM; graph alignment; set of most probable paths Related Software: Sibelia; CAMSA; hybridSPAdes; GTED; HINGE; Canu; Bandage; Unicycler; AGB; Asgan; CYNTENATOR; i-ADHoRe; Minimap2; dipSPAdes; SPAdes Cited in: 2 Publications Standard Articles 1 Publication describing the Software, including 1 Publication in zbMATH Year PathRacer: racing profile HMM paths on assembly graph. Zbl 1416.92118Shlemov, Alexander; Korobeynikov, Anton 2019 Cited by 4 Authors 1 Kolmogorov, Mikhail 1 Korobeynikov, Anton 1 Polevikov, Evgeny 1 Shlemov, Alexander Cited in 0 Serials Cited in 2 Fields 2 Biology and other natural sciences (92-XX) 1 Combinatorics (05-XX) Citations by Year