Results 141 to 150 of about 4,504,319 (408)

Optimizing Data Parallelism for FM-Based Short-Read Alignment on the Heterogeneous Non-Uniform Memory Access Architectures

Future Internet
Sequence alignment is a critical factor in the variant analysis of genomic research. Since the FM (Ferrainas–Manzini) index was developed, it has proven to be a model in a compact format with efficient pattern matching and high-speed query searching ...
Shaolong Chen, Yunzi Dai, Liwei Liu, Xinting Yu   +3 more
doaj   +1 more source

An Alignment Algorithm for Sequences [PDF]

arXiv, 2012
This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or other considerations.
arxiv  

Sequence Transduction with Recurrent Neural Networks [PDF]

, 2012
Many machine learning tasks can be expressed as the transformation---or \emph{transduction}---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few ...
Graves, Alex
core  

Process-oriented Iterative Multiple Alignment for Medical Process Mining

, 2017
Adapted from biological sequence alignment, trace alignment is a process mining technique used to visualize and analyze workflow data. Any analysis done with this method, however, is affected by the alignment quality.
Burd, Randall S., Chen, Shuhong, Marsic, Ivan, Yang, Sen, Zhou, Moliang   +4 more
core   +1 more source

Sequence Alignment

Bioinformatics in Rice Research, 2018
Let x = (x1 . . . xm) and y = (y1 . . . yn) be two sequences of tokens, aka. strings. We assume the lengths m,n are known and a pair of tokens can be compared in constant time.
Manoj Kumar Gupta, G. Gouda, N. Rajesh, R. Donde, S. Sabarinathan, P. Pati, S. K. Rathore, Ramakrishna Vadde, L. Behera   +8 more
semanticscholar   +1 more source

MET variants with activating N‐lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation

Molecular Oncology, EarlyView.
MET variants in the N‐lobe of the kinase domain, found in hereditary papillary renal cell carcinoma, require ligand stimulation to promote cell transformation, in contrast to other RTK variants. This suggests that HGF expression in the microenvironment is important for tumor growth in such patients. Their sensitivity to MET inhibitors opens the way for
Célia Guérin, Audrey Vinchent, Marie Fernandes, Isabelle Damour, Agathe Laratte, Rémi Tellier, Gabriella O. Estevam, Jean‐Pascal Meneboo, Céline Villenet, Clotilde Descarpentries, James S. Fraser, Martin Figeac, Alexis B. Cortot, Etienne Rouleau, David Tulasne   +14 more
wiley   +1 more source

Edlib: a C/C++ library for fast, exact sequence alignment using edit distance

bioRxiv, 2016
We present Edlib, an open-source C/C++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality, and can also easily handle very large ...
Martin Sosic, M. Šikić
semanticscholar   +1 more source

Response to neoadjuvant chemotherapy in early breast cancers is associated with epithelial–mesenchymal transition and tumor‐infiltrating lymphocytes

Molecular Oncology, EarlyView.
Epithelial–mesenchymal transition (EMT) and tumor‐infiltrating lymphocytes (TILs) are associated with early breast cancer response to neoadjuvant chemotherapy (NAC). This study evaluated EMT and TIL shifts, with immunofluorescence and RNA sequencing, at diagnosis and in residual tumors as potential biomarkers associated with treatment response.
Françoise Derouane, Jérôme Ambroise, Cédric van Marcke, Mieke Van Bockstal, Martine Berlière, Christine Galant, Hélène Dano, Médina Lougué, Elena Benidovskaya, Guy Jerusalem, Vincent Bours, Claire Josse, Jérôme Thiry, Aurélie Daumerie, Caroline Bouzin, Cyril Corbet, François P. Duhoux   +16 more
wiley   +1 more source

Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences

Algorithms
The standard approach for constructing a phylogenetic tree from a set of sequences consists of two key stages. First, a multiple sequence alignment (MSA) of the sequences is computed.
Mahbubeh Askari Rad, Alibek Kruglikov, Xuhua Xia   +2 more
doaj   +1 more source

Letter Change Bias and Local Uniqueness in Optimal Sequence Alignments [PDF]

, 2013
Considering two optimally aligned random sequences, we investigate the effect on the alignment score caused by changing a random letter in one of the two sequences. Using this idea in conjunction with large deviations theory, we show that in alignments with a low proportion of gaps the optimal alignment is locally unique in most places with high ...
arxiv   +1 more source