Motivation: Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units.
Results: CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimized alignments as standards of truth. CORAL improves alignment accuracy on core regions over general profile methods, returning a balanced score of 0.57 for over 80% of all domain families in CDD, compared with the highest balanced score of 0.45 from other methods. Further, CORAL provides E-values to aid in detecting homologous protein families and, by respecting block boundaries, produces alignments with improved 'readability' that facilitate manual refinement.
Availability: CORAL will be included in future versions of the NCBI Cn3D/CDTree software, which can be downloaded at http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml.
Supplementary Information: Supplementary data are available at Bioinformatics online.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712342 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btp334 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
NFKB1 as a key player in Tumor biology: from mechanisms to therapeutic implications.
Cell Biol Toxicol
January 2025
Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang , Liaoning Province, China.
NFKB1, a core transcription factor critical in various biological process (BP), is increasingly studied for its role in tumors. This research combines literature reviews, meta-analyses, and bioinformatics to systematically explore NFKB1's involvement in tumor initiation and progression. A unique focus is placed on the NFKB1-94 ATTG promoter polymorphism, highlighting its association with cancer risk across diverse genetic models and ethnic groups, alongside comprehensive analysis of pan-cancer expression patterns and drug sensitivity.
View Article and Find Full Text PDFMorphology of the Soft Palate Tonsil Mucosa of Collared Peccary (Pecari tajacu, Linnaeus, 1758).
Anat Histol Embryol
January 2025
Laboratório de Morfologia e Atividade Física, São Paulo State University, Rio Claro, São Paulo, Brazil.
Collared Peccary (Pecari tajacu, Linnaeus, 1758) is a mammalian Tayassuidae species from tropical to semi-arid areas. The morphological features of the oral cavity in this species were identified and described. Tonsils are secondary lymphoid organs essential for contact with antigens due to food and air intake.
View Article and Find Full Text PDFA Comparative Analysis of Explainable Artificial Intelligence Models for Electric Field Strength Prediction over Eight European Cities.
Sensors (Basel)
December 2024
2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece.
The widespread propagation of wireless communication devices, from smartphones and tablets to Internet of Things (IoT) systems, has become an integral part of modern life. However, the expansion of wireless technology has also raised public concern about the potential health risks associated with prolonged exposure to electromagnetic fields. Our objective is to determine the optimal machine learning model for constructing electric field strength maps across urban areas, enhancing the field of environmental monitoring with the aid of sensor-based data collection.
View Article and Find Full Text PDFDWI in the Differentiation of Malignant and Benign Breast Lesions Presenting with Non-Mass Enhancement on CE-MRI.
Cancers (Basel)
December 2024
Department of Diagnostic and Interventional Radiology, University Hospital Split, Spinčićeva 1, 21000 Split, Croatia.
Article Synopsis
- The study examined if ADC map values of breast lesions with non-mass enhancement on MRI could distinguish between benign and malignant cases.
- A total of 136 patients underwent ultrasound-guided biopsies, and radiologists measured ADC values independently, comparing results to pathology reports.
- The whole tumor region of interest (ROI) showed the highest sensitivity at 91% for detecting benign lesions, while there were no significant ADC value differences between fatty and dense breast tissues.
Two Novel Mouse Models of Duchenne Muscular Dystrophy with Similar Dmd Exon 51 Frameshift Mutations and Varied Phenotype Severity.
Int J Mol Sci
December 2024
Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.
Duchenne muscular dystrophy (DMD) is a severe X-linked genetic disorder caused by an array of mutations in the dystrophin gene, with the most commonly mutated regions being exons 48-55. One of the several existing approaches to treat DMD is gene therapy, based on alternative splicing and mutant exon skipping. Testing of such therapy requires animal models that carry mutations homologous to those found in human patients.
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!