Results 21 to 30 of about 2,954,117 (341)
Contact-based sequence alignment [PDF]
Nucleic Acids Research, 2004 This paper introduces the novel method of contact-based protein sequence alignment, where structural information in the form of contact mutation probabilities is incorporated into an alignment routine using contact-mutation matrices (CAO: Contact Accepted mutatiOn).
Kleinjung, J. +3 more
openaire +3 more sources
Local alignment of two-base encoded DNA sequence
BMC Bioinformatics, 2009 Background DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base ...
Merriman Barry +2 more
doaj +1 more source
Local alignment of generalized
BMC Bioinformatics, 2010 Background DNA sequence comparison is a well-studied problem, in which two DNA sequences are compared using a weighted edit distance. Recent DNA sequencing technologies however observe an encoded form of the sequence, rather than each DNA base ...
Nelson Stanley F +2 more
doaj +1 more source
Sequence-Based Anytime Control
IEEE Transactions on Automatic Control, 2013 We present two related anytime algorithms for control of nonlinear systems when the processing resources available are time-varying. The basic idea is to calculate tentative control input sequences for as many time steps into the future as allowed by the available processing resources at every time step.
Quevedo, Daniel E., Gupta, Vijay
openaire +4 more sources
DddA homolog search and engineering expand sequence compatibility of mitochondrial base editing
Nature Communications, 2023 There is a need to improve and expand mitochondrial base editing tools. Here the authors identify a DddA homolog from Simiaoa sunii (Ddd_Ss) which can efficiently deaminate cytosine in dsDNA; they develop cytosine base editors and introduce mutations at ...
Li Mi +13 more
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Life, 2022 DNA carries more than the list of biochemical ingredients that drive the basic functions of living systems. The sequence of base pairs includes a multitude of structural and energetic signals, which determine the degree to which the long, threadlike ...
Robert T. Young +4 more
doaj +1 more source
Base sequence dependent sliding of proteins on DNA [PDF]
, 2004 The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered.
A. Travers +7 more
core +3 more sources
Journal of Nucleic Acids, 2023 MGB polyamide-oligonucleotide conjugates ON 1-4 with linked MGB polyamides at the 2-exocyclic amino group of a guanine base using aminoalkyl linkers were synthesized and evaluated in terms of binding affinity for complementary DNA containing the MGB ...
Kazuo Kamaike +13 more
doaj +1 more source
Sequence-dependent base pair stepping dynamics in XPD helicase unwinding
eLife, 2013 Helicases couple the chemical energy of ATP hydrolysis to directional translocation along nucleic acids and transient duplex separation. Understanding helicase mechanism requires that the basic physicochemical process of base pair separation be ...
Zhi Qi +3 more
doaj +1 more source
On Logarithmically Benford Sequences [PDF]
, 2015 Let $\mathcal{I} \subset \mathbb{N}$ be an infinite subset, and let $\{a_i\}_{i \in \mathcal{I}}$ be a sequence of nonzero real numbers indexed by $\mathcal{I}$ such that there exist positive constants $m, C_1$ for which $|a_i| \leq C_1 \cdot i^m$ for ...
Chen, Evan +2 more
core +1 more source