A5001696546- Algorithms and Data Compression
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Genome Rearrangement Algorithms
- Advanced Proteomics Techniques and Applications
- Coding theory and cryptography
- graph theory and CDMA systems
Universidade Federal de Mato Grosso do Sul
2018-2024
Abstract In computational biology, mapping a sequence s onto graph G poses significant challenge. One possible approach to tackling this problem is find walk p in that spells most similar . This challenge formally known as the Graph Sequence Mapping Problem ( GSMP ). paper, we delve into an alternative formulation De Bruijn BSMP Both problems have three variants: changes only sequence, graph, and both graph. We concentrate on addressing variant involving literature, when does not allow...
Abstract In computational biology, mapping a sequence s onto graph G is significant challenge. One possible approach to addressing this problem identify walk p in that spells which most similar . This known as the Graph Sequence Mapping Problem ( GSMP ). paper, we study an alternative formulation, namely De Bruijn BSMP ), can be stated follows: given and k (where ≥ 2), find according distance metric. We present both exact algorithms approximate heuristics for solving problem, using edit...
Given two sets of sequences A and B, the Substring Specific problem is to find all minimum substrings in having distance at least k for each subsequence B. This work addresses three new implementations Maaß algorithm when Hamming considered: a naive cubic-time quadratic-time algorithms. We run tests compare running time these another recently described implementation that uses edit distance. In addition, we conducted preliminary testing on large Tara Ocean database, looking efficient...
An important problem in Computational Biology is to determine genetic markers, substrings of a set sequences that do not occur on other sets. Applications for this include finding small specific regions primer design and find organisms or metagenomes. Genetic markers can be addressed by the Specific Substring Problem - SSP which consists all minimal given with at least k differences among another sequence set. Since spend quadratic time when Hamming distance considered we have, general,...