Results 131 to 140 of about 4,504,319 (408)
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
Sequence alignment and mutual information [PDF]
arXiv, 2008 Background: Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. All existing alignment algorithms rely on heuristic scoring schemes based on biological expertise. Therefore, these algorithms do not provide model independent and objective measures for how similar two (or more ...
arxiv
Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification [PDF]
, 2014 Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature
arxiv +1 more source
Molecular Oncology, EarlyView.Analysis of ESR1 mutations in plasma cell‐free DNA (cfDNA) is highly important for the selection of treatment in patients with breast cancer. Using multiplex‐ddPCR and identical blood draws, we investigated whether circulating tumor cells (CTCs) and cfDNA provide similar or complementary information for ESR1 mutations.
Stavroula Smilkou +11 more
wiley +1 more source
Ancestral sequence alignment under optimal conditions
BMC Bioinformatics, 2005 Background Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs
Brown Daniel G, Hudek Alexander K
doaj +1 more source
Multiple sequence alignment for short sequences [PDF]
arXiv, 2015 Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of this problem, the research on this topic is focused on aligning long sequences.
arxiv
Molecular Oncology, EarlyView.Triacsin C inhibition of the acyl‐CoA synthetase long chain (ACSL) family decreases multiple myeloma cell survival, proliferation, mitochondrial respiration, and membrane potential. Made with Biorender.com. Multiple myeloma (MM) is an incurable cancer of plasma cells with a 5‐year survival rate of 59%.
Connor S. Murphy +12 more
wiley +1 more source
Alignment Metric Accuracy [PDF]
arXiv, 2005 We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon previous approaches, and provides a balanced assessment of the fidelity of both matches and gaps.
arxiv
MAFFT-DASH: integrated protein sequence and structural alignment
Nucleic Acids Res., 2019 Here, we describe a web server that integrates structural alignments with the MAFFT multiple sequence alignment (MSA) tool. For this purpose, we have prepared a web-based Database of Aligned Structural Homologs (DASH), which provides structural ...
John Rozewicki +4 more
semanticscholar +1 more source
Molecular Oncology, EarlyView.Prostate cancer is a leading malignancy with significant clinical heterogeneity in men. An 11‐gene signature derived from dysregulated epithelial cell markers effectively predicted biochemical recurrence‐free survival in patients who underwent radical surgery or radiotherapy.
Zhuofan Mou, Lorna W. Harries
wiley +1 more source