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New Genetic Markers Differentiating IPEC and ExPEC Pathotypes—A New Approach to Genome-Wide Analysis Using a New Bioinformatics Tool

The increasingly expanding genomic databases generate the need for new tools for their processing and further use. In the paper, a bioinformatics tool, which is a search engine of microsatellite elements—trinucleotide repeat sequences (TRS) in files of FASTA type—is presented. An innovative approach...

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Detalles Bibliográficos
Autores principales: Majchrzak, Marta, Sakowski, Sebastian, Waldmajer, Jacek, Parniewski, Pawel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10002601/
https://www.ncbi.nlm.nih.gov/pubmed/36902111
http://dx.doi.org/10.3390/ijms24054681
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author Majchrzak, Marta
Sakowski, Sebastian
Waldmajer, Jacek
Parniewski, Pawel
author_facet Majchrzak, Marta
Sakowski, Sebastian
Waldmajer, Jacek
Parniewski, Pawel
author_sort Majchrzak, Marta
collection PubMed
description The increasingly expanding genomic databases generate the need for new tools for their processing and further use. In the paper, a bioinformatics tool, which is a search engine of microsatellite elements—trinucleotide repeat sequences (TRS) in files of FASTA type—is presented. An innovative approach was applied in the tool, which consists of connecting—within one search engine—both mapping of TRS motifs and extracting sequences that are found between the mapped TRS motifs. Accordingly, we present hereby the tool called TRS-omix, which comprises a new engine for searching information on genomes and enables generation of sets of sequences and their number, providing the basis for making comparisons between genomes. In our paper, we showed one of the possibilities of using the software. Using TRS-omix and other IT tools, we showed that we were able to extract sets of DNA sequences that can be assigned only to the genomes of the extraintestinal pathogenic Escherichia coli strains or to the genomes of the intestinal pathogenic Escherichia coli strains, as well as providing the basis for differentiation of the genomes/strains belonging to each of these clinically essential pathotypes.
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spelling pubmed-100026012023-03-11 New Genetic Markers Differentiating IPEC and ExPEC Pathotypes—A New Approach to Genome-Wide Analysis Using a New Bioinformatics Tool Majchrzak, Marta Sakowski, Sebastian Waldmajer, Jacek Parniewski, Pawel Int J Mol Sci Article The increasingly expanding genomic databases generate the need for new tools for their processing and further use. In the paper, a bioinformatics tool, which is a search engine of microsatellite elements—trinucleotide repeat sequences (TRS) in files of FASTA type—is presented. An innovative approach was applied in the tool, which consists of connecting—within one search engine—both mapping of TRS motifs and extracting sequences that are found between the mapped TRS motifs. Accordingly, we present hereby the tool called TRS-omix, which comprises a new engine for searching information on genomes and enables generation of sets of sequences and their number, providing the basis for making comparisons between genomes. In our paper, we showed one of the possibilities of using the software. Using TRS-omix and other IT tools, we showed that we were able to extract sets of DNA sequences that can be assigned only to the genomes of the extraintestinal pathogenic Escherichia coli strains or to the genomes of the intestinal pathogenic Escherichia coli strains, as well as providing the basis for differentiation of the genomes/strains belonging to each of these clinically essential pathotypes. MDPI 2023-02-28 /pmc/articles/PMC10002601/ /pubmed/36902111 http://dx.doi.org/10.3390/ijms24054681 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Majchrzak, Marta
Sakowski, Sebastian
Waldmajer, Jacek
Parniewski, Pawel
New Genetic Markers Differentiating IPEC and ExPEC Pathotypes—A New Approach to Genome-Wide Analysis Using a New Bioinformatics Tool
title New Genetic Markers Differentiating IPEC and ExPEC Pathotypes—A New Approach to Genome-Wide Analysis Using a New Bioinformatics Tool
title_full New Genetic Markers Differentiating IPEC and ExPEC Pathotypes—A New Approach to Genome-Wide Analysis Using a New Bioinformatics Tool
title_fullStr New Genetic Markers Differentiating IPEC and ExPEC Pathotypes—A New Approach to Genome-Wide Analysis Using a New Bioinformatics Tool
title_full_unstemmed New Genetic Markers Differentiating IPEC and ExPEC Pathotypes—A New Approach to Genome-Wide Analysis Using a New Bioinformatics Tool
title_short New Genetic Markers Differentiating IPEC and ExPEC Pathotypes—A New Approach to Genome-Wide Analysis Using a New Bioinformatics Tool
title_sort new genetic markers differentiating ipec and expec pathotypes—a new approach to genome-wide analysis using a new bioinformatics tool
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10002601/
https://www.ncbi.nlm.nih.gov/pubmed/36902111
http://dx.doi.org/10.3390/ijms24054681
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