CrossLink is a versatile tool for the exploration of relationships between RNA sequences. After a parametrization phase, CrossLink delegates the determination of sequence relationships to established tools (BLAST, Vmatch and RNAhybrid) and then constructs a network. Each node in this network represents a sequence and each link represents a match or a set of matches. Match attributes are reflected by graphical attributes of the links and corresponding alignments are displayed on a mouse-click. The distributions of match attributes such as E-value, match length and proportion of identical nucleotides are displayed as histograms. Sequence sets can be highlighted and visibility of designated matches can be suppressed by real-time adjustable thresholds for attribute combinations. Powerful network layout operations (such as spring-embedding algorithms) and navigation capabilities complete the exploration features of this tool. CrossLink can be especially useful in a microRNA context since Vmatch and RNAhybrid are suitable tools for determining the antisense and hybridization relationships, which are decisive for the interaction between microRNAs and their targets. CrossLink is available both online and as a standalone version at http://www-ab.informatik.uni-tuebingen.de/software.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538911 | PMC |
| http://dx.doi.org/10.1093/nar/gkl223 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Development of targeted antimicrobial peptides for Escherichia coli: Combining phage display and rational design for food safety application.
Food Chem
December 2024
Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China. Electronic address:
The growing demand for minimally processed foods has heightened the risk of pathogenic contamination. Balancing antimicrobial efficacy with the preservation of probiotic activity remains a significant challenge. In this study, we employed phage display peptide library screening, combined with next-generation sequencing to identify the HIMPIQA domain, which selectively targets pathogenic Escherichia coli (E.
View Article and Find Full Text PDFFirst identification and whole genome characterization of rotavirus C in pigs in Zambia.
Virology
December 2024
Institute for Vaccine Research and Development, Hokkaido University, Sapporo, 001-0021, Japan; Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, 10101, Zambia; One Health Research Center, Hokkaido University, Sapporo, 060-0818, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan; Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, 10101, Zambia. Electronic address:
Rotavirus C (RVC) causes acute gastroenteritis in neonatal piglets. Despite the clinical importance of RVC infection, the distribution and prevalence in pig populations in most African countries remains unknown. In this study, we identified RVC in Zambian pigs by metagenomic analysis.
View Article and Find Full Text PDFPredicting phage-host interactions via feature augmentation and regional graph convolution.
Brief Bioinform
November 2024
Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University, Wuhan 430079, China.
Identifying phage-host interactions (PHIs) is a crucial step in developing phage therapy, which is the promising solution to addressing the issue of antibiotic resistance in superbugs. However, the lifestyle of phages, which strongly depends on their host for life activities, limits their cultivability, making the study of predicting PHIs time-consuming and labor-intensive for traditional wet lab experiments. Although many deep learning (DL) approaches have been applied to PHIs prediction, most DL methods are predominantly based on sequence information, failing to comprehensively model the intricate relationships within PHIs.
View Article and Find Full Text PDFDiversity and antimicrobial resistance profiles of Mycobacterium avium complex clinical isolates in Thailand based on whole genome comparative analysis.
Sci Rep
January 2025
Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
The Mycobacterium avium complex (MAC) is a group of closely related nontuberculous mycobacteria that can cause various diseases in humans. In this study, genome sequencing, comprehensive genomic analysis, and antimicrobial susceptibility testing of 66 MAC clinical isolates from King Chulalongkorn Memorial Hospital, Bangkok, Thailand were carried out. Whole-genome average nucleotide identity (ANI) revealed the MAC species distribution, comprising 54 (81.
View Article and Find Full Text PDFChromosome-level genome assembly of Salvia sclarea.
Sci Data
January 2025
Department of Crop Science, Chungnam National University, Daejeon, 34134, Korea.
Salvia sclarea is a medicinal herb from the Lamiaceae family, valued for its essential oil which contains sclareol, linalool, linalyl acetate, and other compounds. Despite its extensive use, the genetic mechanisms of S. sclarea are not well understood.
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!