RNAmountAlign: efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment [PDF]
arXiv, 2018 Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for structural homology identi^Lcation.
arxiv
Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments [PDF]
, 1998 Ángel R. Ortíz +2 more
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Molecular Oncology, EarlyView.Chronic TGF‐β exposure drives epithelial HCC cells from a senescent state to a TGF‐β resistant mesenchymal phenotype. This transition is characterized by the loss of Smad3‐mediated signaling, escape from senescence, enhanced invasiveness and metastatic potential, and upregulation of key resistance modulators such as MARK1 and GRM8, ultimately promoting
Minenur Kalyoncu +11 more
wiley +1 more source
HMMerge: an ensemble method for multiple sequence alignment. [PDF]
Bioinform Adv, 2023 Park M, Warnow T.
europepmc +1 more source
MulBlast 1.0: a multiple alignment of BLAST output to boost protein sequence similarity analysis [PDF]
, 1996 Gilles Labesse
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HAlign: Fast multiple similar DNA/RNA sequence alignment based on the centre star strategy
Bioinform., 2015 MOTIVATION Multiple sequence alignment (MSA) is important work, but bottlenecks arise in the massive MSA of homologous DNA or genome sequences. Most of the available state-of-the-art software tools cannot address large-scale datasets, or they run rather ...
Q. Zou +3 more
semanticscholar +1 more source
Molecular Oncology, EarlyView.We identified adaptor protein ShcD as upregulated in triple‐negative breast cancer and found its expression to be correlated with reduced patient survival and increased invasion in cell models. Using a proteomic screen, we identified novel ShcD binding partners involved in EGFR signaling pathways.
Hayley R. Lau +11 more
wiley +1 more source
Multiple sequence alignment based on deep reinforcement learning with self-attention and positional encoding. [PDF]
Bioinformatics, 2023 Liu Y +6 more
europepmc +1 more source
Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions [PDF]
, 1999 Nikola M. Stojanović
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Statistical Methods for Conservation and Alignment Quality in Proteins [PDF]
, 2008 Construction of multiple sequence alignments is a fundamental task in Bioinformatics. Multiple sequence alignments are used as a prerequisite in many Bioinformatics methods, and subsequently the quality of such methods can be critically dependent on the ...
Ahola, Virpi
core