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
Algorithms for Nucleic Acid Sequence Design [PDF]
, 2010 Motivated by a growing field of research focused on programming function into biomolecules, we seek to decrease the cost of high-quality rational nucleic acid sequence design while increasing its versatility and availability.
Zadeh, Joseph N.
core +1 more source
QTrim : a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform [PDF]
, 2014 Background Many high throughput sequencing (HTS) approaches, such as the Roche/454 platform, produce sequences in which the quality of the sequence (as measured by a Phred-like quality scores) decreases linearly across a sequence read.
Grace P McCormack +11 more
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PSALR : Parallel Sequence Alignment for long Sequence Read with Hash Model [PDF]
Journal of Artificial Intelligence and Data MiningSequence alignment and genome mapping pose significant challenges, primarily focusing on speed and storage space requirements for mapped sequences. With the ever-increasing volume of DNA sequence data, it becomes imperative to develop efficient alignment
Nasrin Aghaee-Maybodi +3 more
doaj +1 more source
Evaluation of nucleosome forming potentials (NFPs) of forensically important STRs [PDF]
, 2011 Degraded forensic samples have proved difficult to analyze and interpret. New analysis techniques are constantly being discovered and improved but researchers have overlooked the structural properties that could prevent or slow the process of degradation.
Thanakiatkrai, Phuvadol +3 more
core +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
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
doaj +1 more source
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
Anatomy and origin of authochthonous late Pleistocene forced regression deposits, east Coromandel inner shelf, New Zealand: implications for the development and definition of the regressive systems tract [PDF]
, 2004 High-resolution seismic reflection data from the east Coromandel coast, New Zealand, provide details of the sequence stratigraphy beneath an autochthonous, wave dominated inner shelf margin during the late Quaternary (0-140 ka). Since c.
Nelson, Campbell S. +3 more
core +1 more source
Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes
Viruses, 2018 Base-By-Base is a comprehensive tool for the creation and editing of multiple sequence alignments that is coded in Java and runs on multiple platforms. It can be used with gene and protein sequences as well as with large viral genomes, which themselves ...
Shin-Lin Tu +5 more
doaj +1 more source