{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:56:27Z","timestamp":1760147787704,"version":"build-2065373602"},"reference-count":21,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2023,2,28]],"date-time":"2023-02-28T00:00:00Z","timestamp":1677542400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"IMB PAS"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>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\u2014trinucleotide repeat sequences (TRS) in files of FASTA type\u2014is presented. An innovative approach was applied in the tool, which consists of connecting\u2014within one search engine\u2014both 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.<\/jats:p>","DOI":"10.3390\/ijms24054681","type":"journal-article","created":{"date-parts":[[2023,2,28]],"date-time":"2023-02-28T06:09:52Z","timestamp":1677564592000},"page":"4681","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["New Genetic Markers Differentiating IPEC and ExPEC Pathotypes\u2014A New Approach to Genome-Wide Analysis Using a New Bioinformatics Tool"],"prefix":"10.3390","volume":"24","author":[{"given":"Marta","family":"Majchrzak","sequence":"first","affiliation":[{"name":"Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Str., 93-232 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6127-3403","authenticated-orcid":false,"given":"Sebastian","family":"Sakowski","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics and Computer Science, University of Lodz, Banacha 22, 90-238 Lodz, Poland"},{"name":"Centre for Data Analysis, Modelling and Computational Sciences, University of Lodz, Scheibler Family Avenue 2, 90-128 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5303-7665","authenticated-orcid":false,"given":"Jacek","family":"Waldmajer","sequence":"additional","affiliation":[{"name":"Institute of Computer Science, University of Opole, Oleska 48, 45-052 Opole, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9074-2758","authenticated-orcid":false,"given":"Pawel","family":"Parniewski","sequence":"additional","affiliation":[{"name":"Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Str., 93-232 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,2,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1016\/0959-437X(94)90067-1","article-title":"Simple sequences","volume":"4","author":"Tautz","year":"1994","journal-title":"Curr. 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