Results 71 to 80 of about 4,504,319 (408)

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

Bioinform., 2016
MOTIVATION Many biological processes are guided by receptor interactions with linear ligands of variable length. One such receptor is the MHC class I molecule. The length preferences vary depending on the MHC allele, but are generally limited to peptides
M. Andreatta, M. Nielsen
semanticscholar   +1 more source

Making tau amyloid models in vitro: a crucial and underestimated challenge

FEBS Letters, EarlyView.
This review highlights the challenges of producing in vitro amyloid assemblies of the tau protein. We review how accurately the existing protocols mimic tau deposits found in the brain of patients affected with tauopathies. We discuss the important properties that should be considered when forming amyloids and the benchmarks that should be used to ...
Julien Broc, Clara Piersson, Yann Fichou
wiley   +1 more source

Lower bounds on multiple sequence alignment using exact 3-way alignment

BMC Bioinformatics, 2007
Background Multiple sequence alignment is fundamental. Exponential growth in computation time appears to be inevitable when an optimal alignment is required for many sequences. Exact costs of optimum alignments are therefore rarely computed. Consequently
Colbourn Charles J, Kumar Sudhir
doaj   +1 more source

Alvira : comparative genomics of viral strains [PDF]

, 2007
The Alvira tool is a general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. This new tool has been devised specifically to address the problem of the simultaneous analysis of a large ...
Brodie, Chenna, E. Baranowski, Edgar, F. Enault, Ghedin, Lassmann, Lee, R. Fremez, T. Faraut, Zmasek   +10 more
core   +2 more sources

Aligning two fragmented sequences [PDF]

Proceedings 16th International Parallel and Distributed Processing Symposium, 2002
AbstractUpon completion of the human and mouse genome sequences, world-wide sequencing capacity will turn to other complex organisms. Current strategies call for many of these genomes to be incompletely sequenced. That is, holes will remain in the known sequence, and the relative order and orientation of the known sequence fragments may not be ...
Piotr Berman, Vamsi Veeramachaneni, Webb Miller   +2 more
openaire   +3 more sources

Refining the NaV1.7 pharmacophore of a class of venom‐derived peptide inhibitors via a combination of in silico screening and rational engineering

FEBS Letters, EarlyView.
Venom peptides have shown promise in treating pain. Our study uses computer screening to identify a peptide that targets a sodium channel (NaV1.7) linked to chronic pain. We produced the peptide in the laboratory and refined its design, advancing the search for innovative pain therapies.
Gagan Sharma, Jennifer R. Deuis, Xinying Jia, Theo Crawford, Sassan Rahnama, Eivind A. B. Undheim, Irina Vetter, Yanni K. ‐Y. Chin, Mehdi Mobli   +8 more
wiley   +1 more source

Pairwise alignment incorporating dipeptide covariation

, 2005
Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated.
Altschul, Altschul, Altschul, Altschul, Bailey, Bishop, Brenner, Cline, Crooks, DOOLITTLE, Frith, Fukami-Kobayashi, G. E. Crooks, Goldman, Gonnet, Henikoff, Henikoff, Jung, Karplus, Lin, Muller, Murzin, Park, Pearson, R. E. Green, RODIONOV, S. E. Brenner, Sander, Smith, Thorne, Thorne, Thorne, Topham, Weiss, Zachariah   +34 more
core   +1 more source

Mauve: multiple alignment of conserved genomic sequence with rearrangements.

Genome Research, 2004
As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into ...
A. Darling, B. Mau, F. Blattner, N. Perna   +3 more
semanticscholar   +1 more source

Informer: Beyond Efficient Transformer for Long Sequence Time-Series Forecasting [PDF]

AAAI Conference on Artificial Intelligence, 2020
Many real-world applications require the prediction of long sequence time-series, such as electricity consumption planning. Long sequence time-series forecasting (LSTF) demands a high prediction capacity of the model, which is the ability to capture ...
Haoyi Zhou, Shanghang Zhang, Jieqi Peng, Shuai Zhang, Jianxin Li, Hui Xiong, Wan Zhang   +6 more
semanticscholar   +1 more source

The effect of sequence quality on sequence alignment [PDF]

Bioinformatics, 2008
Abstract Motivation: The nucleotide sequencing process produces not only the sequence of nucleotides, but also associated quality values. Quality values provide valuable information, but are primarily used only for trimming sequences and generally ignored in subsequent analyses.
openaire   +3 more sources