Background: Tandem repeats are specific sequences in genomic DNA repeated in tandem that are present in all organisms. Among the subcategories of TRs we have Satellite repeats, that is divided into macrosatellites, minisatellites, and microsatellites, being the last two of specific interest because they can identify polymorphisms between organisms due to their instability. Currently, most mining tools focus on Simple Sequence Repeats (SSR) mining, and only a few can identify SSRs in the coding regions.
Results: We developed a microsatellite mining software called SATIN (Micro and Mini SATellite IdentificatioN tool) based on a new sliding window algorithm written in C and Python. It represents a new approach to SSR mining by addressing the limitations of existing tools, particularly in coding region SSR mining. SATIN is available at https://github.com/labgm/SATIN.git . It was shown to be the second fastest for perfect and compound SSR mining. It can identify SSRs from coding regions plus SSRs with motif sizes bigger than 6. Besides the SSR mining, SATIN can also analyze SSRs polymorphism on coding-regions from pre-determined groups, and identify SSRs differentially abundant among them on a per-gene basis. To validate, we analyzed SSRs from two groups of Escherichia coli (K12 and O157) and compared the results with 5 known SSRs from coding regions. SATIN identified all 5 SSRs from 237 genes with at least one SSR on it.
Conclusions: The SATIN is a novel microsatellite search software that utilizes an innovative sliding window technique based on a numerical list for repeat region search to identify perfect, and composite SSRs while generating comprehensible and analyzable outputs. It is a tool capable of using files in fasta or GenBank format as input for microsatellite mining, also being able to identify SSRs present in coding regions for GenBank files. In conclusion, we expect SATIN to help identify potential SSRs to be used as genetic markers.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11186120 | PMC |
| http://dx.doi.org/10.1186/s12859-024-05842-2 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Reactivation of hidden-latent infection after doxycycline and streptomycin treatment in mice.
Antimicrob Agents Chemother
December 2024
Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica.
Brucellosis has therapeutic challenges due to 3%-15% relapses/therapeutic failures (R/TF) after antibiotic treatment. Therefore, determining the antibiotic concentration in tissues, the physiopathological parameters, and the R/TF after treatment is relevant. After exploring different antibiotic quantities, we found that a combined dose of 100 µg/g of doxycycline (for 45 days) and 7.
View Article and Find Full Text PDF[Genomic Characterization of SARS-CoV-2 Isolates Obtained from Antalya, Türkiye].
Mikrobiyol Bul
October 2024
The University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, Netherlands.
As the number of coronavirus diseases-2019 (COVID-19) cases have decreased and measures have started to be implemented at an individual level rather than in the form of social restrictions, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) still maintains its importance and has already taken its place in the spectrum of agents investigated in multiplex molecular test panels for respiratory tract infections in routine diagnostic use. In this study, we aimed to present mutation analysis and clade distribution of whole genome sequences from randomly selected samples that tested positive with SARS-CoV-2 specific real-time reverse transcription polymerase chain reaction (rRT-PCR) test at different periods of the pandemic in our laboratory with a commercial easy-to-use kit designed for next-generation sequencing systems. A total of 84 nasopharyngeal/oropharyngeal swab samples of COVID-19 suspected patients which were sent for routine diagnosis to the medical microbiology laboratory and detected as SARSCoV-2 RNA positive with rRT-PCR were randomly selected from different periods for sequence analysis.
View Article and Find Full Text PDFRecombinant avian metapneumovirus subtype C expressing HA protein of H9N2 avian influenza virus are stable and induce protection.
Front Microbiol
December 2024
Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
To prevent H9N2 avian influenza virus (AIV) and Avian metapneumonovirus/C (aMPV/C) infections, we constructed recombinant aMPV/C viruses expressing the HA protein of H9N2 AIV. In addition, EGFP was inserted into the intermediate non-coding region of P-M protein in the aMPV/C genome using a reverse genetic system. The conditions for rescuing the recombinant virus were enhanced followed by insertion of the H9N2 AIV HA gene into the same location in the aMPV/C.
View Article and Find Full Text PDFValue of using the ICF Core Set for patients with Musculoskeletal Conditions in Outpatient Rehabilitation Facilities in South-Eastern Poland.
Ann Agric Environ Med
December 2024
Institute of Medical Sciences, College of Medical Sciences of the University of Rzeszów, Poland.
Introduction And Objective: A biopsychosocial model for assessing the functioning of patients with musculoskeletal diseases is essential for planning health services for this patient group. For this purpose, the International Classification of Functioning, Disability and Health (ICF) and the 'core sets' created on its basis are used. The aim of this study was to validate and evaluate the effectiveness of the application of the ICF classification in the assessment of patients with musculoskeletal problems in outpatient rehabilitation facilities.
View Article and Find Full Text PDFInsight into the evolution of phosphorous conversion, microbial community and functional gene expression during anaerobic co-digestion of food waste and excess sludge with spicy substances exposure.
Chemosphere
December 2024
Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, 15 Yucai Road, Guilin 541004, PR China; Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin 541004, PR China. Electronic address:
Garlic and chili are widely used as food flavoring agents in food cooking, therefore might be accumulated in large amounts in food waste (FW). The effects of garlic and chili on the dissolution, hydrolysis, acidification and methanation in an anaerobic co-digestion system were investigated during the combined co-digestion of FW and excess sludge (ES). Additionally, the transformation of phosphorus form and microbial metabolism changes during the process were analyzed.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!