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Finding maximal exact matches in graphs
CONCLUSIONS: We show that seed-chain-extend type of alignment methods can be implemented on top of indexable Elastic Founder Graphs by providing an efficient way to produce the seeds between a set of queries and the graph. The code is available in https://github.com/algbio/efg-mems .PMID:38468275 | PMC:PMC10929130 | DOI:10.1186/s13015-024-00255-5 (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - March 12, 2024 Category: Molecular Biology Authors: Nicola Rizzo Manuel C áceres Veli M äkinen Source Type: research

Finding maximal exact matches in graphs
CONCLUSIONS: We show that seed-chain-extend type of alignment methods can be implemented on top of indexable Elastic Founder Graphs by providing an efficient way to produce the seeds between a set of queries and the graph. The code is available in https://github.com/algbio/efg-mems .PMID:38468275 | DOI:10.1186/s13015-024-00255-5 (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - March 12, 2024 Category: Molecular Biology Authors: Nicola Rizzo Manuel C áceres Veli M äkinen Source Type: research

SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration
CONCLUSION: Our SparseRNAFolD algorithm is an MFE-based algorithm that guarantees optimality of result and employs the most general energy model, including dangle contributions. We provide a basis for applying dangles to sparsified recursion in a pseudoknot-free model that has the potential to be extended to pseudoknots.PMID:38433200 | DOI:10.1186/s13015-024-00256-4 (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - March 3, 2024 Category: Molecular Biology Authors: Mateo Gray Sebastian Will Hosna Jabbari Source Type: research

Recombinations, chains and caps: resolving problems with the DCJ-indel model
Algorithms Mol Biol. 2024 Feb 27;19(1):8. doi: 10.1186/s13015-024-00253-7.ABSTRACTOne of the most fundamental problems in genome rearrangement studies is the (genomic) distance problem. It is typically formulated as finding the minimum number of rearrangements under a model that are needed to transform one genome into the other. A powerful multi-chromosomal model is the Double Cut and Join (DCJ) model.While the DCJ model is not able to deal with some situations that occur in practice, like duplicated or lost regions, it was extended over time to handle these cases. First, it was extended to the DCJ-indel model, solving the...
Source: Algorithms for Molecular Biology : AMB - February 28, 2024 Category: Molecular Biology Authors: Leonard Bohnenk ämper Source Type: research

Unifying duplication episode clustering and gene-species mapping inference
We present a novel problem, called MetaEC, which aims to infer gene-species assignments in a collection of partially leaf-labeled gene trees labels by minimizing the size of duplication episode clustering (EC). This problem is particularly relevant in metagenomics, where incomplete data often poses a challenge in the accurate reconstruction of gene histories. To solve MetaEC, we propose a polynomial time dynamic programming (DP) formulation that verifies the existence of a set of duplication episodes from a predefined set of episode candidates. In addition, we design a method to infer distributions of gene-species mappings...
Source: Algorithms for Molecular Biology : AMB - February 14, 2024 Category: Molecular Biology Authors: Pawe ł Górecki Natalia Rutecka Agnieszka Mykowiecka Jaros ław Paszek Source Type: research