Searching a database for a local alignment to a query under a typical scoring scheme, such as PAM120 or BLOSUM62 with affine gap costs, is a computation that has resisted algorithmic improvement due to its basis in dynamic programming and the weak nature of the signals being searched for. In a query preprocessing step, a set of tables can be built that permit one to (a) eliminate a large fraction of the dynamic programming matrix from consideration and (b) to compute several steps of the remainder with a single table lookup. While this result is not an asymptotic improvement over the original Smith-Waterman algorithm, its complexity is characterized in terms of some sparse features of the matrix and it yields the fastest software implementation to date for such searches.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1089/106652703321825919 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Mitigating triplet loss in 2D WSe/non-fullerene heterostructures using halogenated acceptors.
Mater Horiz
January 2025
Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Straße 24/25, 14476, Germany.
Two-dimensional transition metal dichalcogenides (2D TMDCs) can be combined with organic semiconductors to form hybrid van der Waals heterostructures. Specially, non-fullerene acceptors (NFAs) stand out due to their excellent absorption and exciton diffusion properties. Here, we couple monolayer tungsten diselenide (ML-WSe) with two well performing NFAs, ITIC, and IT-4F (fluorinated ITIC) to achieve hybrid architectures.
View Article and Find Full Text PDFInfinite Mixture Chaining: An Efficiency-Based Framework for the Dynamic Construction of Word Meaning.
Open Mind (Camb)
January 2025
Department of Computer Science, University of Toronto, Toronto, Canada.
The lexicon is an evolving symbolic system that expresses an unbounded set of emerging meanings with a limited vocabulary. As a result, words often extend to new meanings. Decades of research have suggested that word meaning extension is non-arbitrary, and recent work formalizes this process as cognitive models of semantic chaining whereby emerging meanings link to existing ones that are semantically close.
View Article and Find Full Text PDFThe Study of Adolescent Resilience (SOAR): a research protocol.
Front Child Adolesc Psychiatry
March 2024
Military Population Health Directorate, Naval Health Research Center, San Diego, CA, United States.
Background: Adolescence is a particularly sensitive period of development for military-connected youth, given the socioemotional and physical changes that occur against the backdrop of the military career of their parent(s). Military-connected adolescents face unique stressors relative to their civilian counterparts, such as military relocations, parental absence due to deployments and trainings, and parental military-related physical and mental injury. These stressors may change family dynamics and disrupt social support networks, which can have lasting implications for adolescent health and well-being.
View Article and Find Full Text PDFThe importance of group factors in the delivery of group-based parenting programmes: a process evaluation of Mellow Babies.
Front Child Adolesc Psychiatry
June 2024
Centre for Rural Health, Centre for Health Science, University of Aberdeen, Inverness, United Kingdom.
Introduction: The role of the group has been largely overlooked within evaluations of group-based parenting programmes. Group contextual factors, including size and level of homogeneity, may impact on essential group processes, such as group identification and cohesion, that are necessary to activate interpersonal change mechanisms and attain programme outcomes. This process evaluation of Mellow Babies, a 14-week attachment-based group parenting programme for mothers of infants aged under 18 months, explores how group context affected mother and practitioner experiences of the programme.
View Article and Find Full Text PDFIntegrating Network Pharmacology and In Silico Analysis to Explore the Bioactive Compounds Against Gastric Cancer Treatment.
Cureus
December 2024
Community Medicine, Siksha 'O' Anusandhan Deemed to be University Institute of Medical Sciences and SUM Hospital, Bhubaneswar, IND.
Gastric cancer (GC) has become a major challenge in oncology research, primarily due to its detection at advanced stages. In this study, we identified and validated the pharmacological mechanisms involved in treating gastric cancer using an integrated approach combining network pharmacology, molecular docking, and a dynamic approach. Gastric cancer-related genes were obtained from DisGeNET, Genecard, and Malacard databases, while potential targets of bioactive compounds were predicted using SwissTargetPrediction.
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!