Results 101 to 110 of about 1,296,938 (317)

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

Anchor points for genome alignment based on Filtered Spaced Word Matches [PDF]

arXiv, 2017
Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure. Speed and quality of these methods therefore depend on the underlying anchor points.
arxiv  

Integrative transcriptomic analysis identifies emetine as a promising candidate for overcoming acquired resistance to ALK inhibitors in lung cancer

Molecular Oncology, EarlyView.
We propose an efficient strategy to suppress ALK inhibitor (ALKi) resistance. By analyzing transcriptome data, we identified emetine as a potential inhibitor. We demonstrated that emetine exhibited effectiveness in inhibiting the growth of ALKi‐resistant cells, and further interpreted its impact on the resistant signatures through drug‐induced RNA ...
Sang‐Min Park, Keeok Haam, Haejeong Heo, Doyeong Kim, Min‐Ju Kim, Hyo‐Jung Jung, Seongwon Cha, Mirang Kim, Haeseung Lee   +8 more
wiley   +1 more source

Fractal MapReduce decomposition of sequence alignment

Algorithms for Molecular Biology, 2012
Background The dramatic fall in the cost of genomic sequencing, and the increasing convenience of distributed cloud computing resources, positions the MapReduce coding pattern as a cornerstone of scalable bioinformatics algorithm development.
Almeida Jonas S, Grüneberg Alexander, Maass Wolfgang, Vinga Susana   +3 more
doaj   +1 more source

Improving spliced alignment for identification of ortholog groups and multiple CDS alignment [PDF]

arXiv, 2017
The Spliced Alignment Problem (SAP) that consists in finding an optimal semi-global alignment of a spliced RNA sequence on an unspliced genomic sequence has been largely considered for the prediction and the annotation of gene structures in genomes.
arxiv  

Comparing and contrasting Escherichia coli and Mycobacterium tuberculosis mechanosensitive channels (MscL) - New gain of function mutations in the loop region [PDF]

, 2000
Sequence analysis of 35 putative MscL homologues was used to develop an optimal alignment for Escherichia coli and Mycobacterium tuberculosis MscL and to place these homologues into sequence subfamilies.
Dougherty, Dennis A., Elmore, Donald E., Lester, Henry A., Maurer, Joshua A.   +3 more
core  

Cellular liquid biopsy provides unique chances for disease monitoring, preclinical model generation and therapy adjustment in rare salivary gland cancer patients

Molecular Oncology, EarlyView.
We quantified and cultured circulating tumor cells (CTCs) of 62 patients with various cancer types and generated CTC‐derived tumoroid models from two salivary gland cancer patients. Cellular liquid biopsy‐derived information enabled molecular genetic assessment of systemic disease heterogeneity and functional testing for therapy selection in both ...
Nataša Stojanović Gužvić, Florian Lüke, Steffi Treitschke, Andrea Coluccio, Martin Hoffmann, Giancarlo Feliciello, Adithi Ravikumar Varadarajan, Xin Lu, Kathrin Weidele, Catherine Botteron, Silvia Materna–Reichelt, Felix Keil, Katja Evert, Florian Weber, Thomas Schamberger, Michael Althammer, Jirka Grosse, Dirk Hellwig, Christian Schulz, Stephan Seitz, Peter Ugocsai, Anke Schlenska‐Lange, Roman Mayr, Ulrich Kaiser, Wolfgang Dietmaier, Bernhard Polzer, Jens Warfsmann, Kamran Honarnejad, Tobias Pukrop, Daniel Heudobler, Christoph A. Klein, Christian Werno   +31 more
wiley   +1 more source

Multiple Sequence Alignment Menggunakan Hidden Markov Model [PDF]

, 2008
Mudah dan murahnya proses pengumpulan data biologi molekuler saat ini menyebabkan ukuran basis data genetika meningkat dengan pesat. Hal ini meningkatkan kebutuhan akan alat bantu komputasi untuk menganalisa data tersebut.
Afiahayati, A. (Afiahayati), Mulyana, S. (Sri)   +1 more
core  

Combined spatially resolved metabolomics and spatial transcriptomics reveal the mechanism of RACK1‐mediated fatty acid synthesis

Molecular Oncology, EarlyView.
The authors analyzed the spatial distributions of gene and metabolite profiles in cervical cancer through spatial transcriptomic and spatially resolved metabolomic techniques. Pivotal genes and metabolites within these cases were then identified and validated.
Lixiu Xu, Jinqiu Li, Junqi Ma, Ayshamgul Hasim   +3 more
wiley   +1 more source

FPGA-based protein sequence alignment : A review

EPJ Web of Conferences, 2017
Sequence alignment have been optimized using several techniques in order to accelerate the computation time to obtain the optimal score by implementing DP-based algorithm into hardware such as FPGA-based platform.
Md. Isa Mohd. Nazrin, Ku Muhsen Ku Noor Dhaniah, Saiful Nurdin Dayana, Ahmad Muhammad Imran, Zainol Murad Sohiful Anuar, Mohyar Shaiful Nizam, Harun Azizi, Hussin Razaidi   +7 more
doaj   +1 more source