Results 51 to 60 of about 1,276,854 (326)

Reticular alignment: A progressive corner-cutting method for multiple sequence alignment

BMC Bioinformatics, 2010
Background In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table ...
Novák Ádám, Szabó Adrienn, Miklós István, Hein Jotun   +3 more
doaj   +1 more source

Sequence alignment, mutual information, and dissimilarity measures for constructing phylogenies [PDF]

, 2010
Existing sequence alignment algorithms use heuristic scoring schemes which cannot be used as objective distance metrics. Therefore one relies on measures like the p- or log-det distances, or makes explicit, and often simplistic, assumptions about ...
A Kraskov, A Milosavljević, G Navarro, J Felsenstein, J Lake, J Rissanen, J Rissanen, J Thompson, J Varre, Konrad Scheffler, L Allison, M Brudno, M Brudno, M Cao, M Li, M Li, M Mahoney, M Nei, M Steel, Maya Paczuski, N Bray, N Bray, N Saitou, Orion Penner, P Buneman, P Lockhart, P Viola, Peter Grassberger, R Cilibrasi, R Durbin, S Altschul, S Altschul, S McGinnis, S Vinga, T Cover, T Lassmann, W Press, X Chen   +37 more
core   +5 more sources

RAD50 missense variants differentially affect the DNA damage response and mitotic progression

FEBS Letters, EarlyView.
RAD50 incorporates into the MRN complex and initiates the DNA damage response. Furthermore, RAD50 promotes mitotic progression. RAD50 missense variants capable of forming an MRN complex supported the DNA damage response and mitotic features to different extents in complementation experiments, indicating these functions are separable and might impact ...
Hanna Redeker, Swantje Kebel, Lea Völkening, Anna Vatselia, Louisa Weinhold, Girmay Asgedom, Axel Schambach, Detlev Schindler, Thilo Dörk, Kristine Bousset   +9 more
wiley   +1 more source

Bethe Ansatz in the Bernoulli Matching Model of Random Sequence Alignment

, 2008
For the Bernoulli Matching model of sequence alignment problem we apply the Bethe ansatz technique via an exact mapping to the 5--vertex model on a square lattice.
A. M. Vershik, D. Gusfield, D. Sankoff, J. M. Hammersley, Kirone Mallick, M. Ablowitz, M. S. Waterman, R. Dubrin, R. J. Baxter, R. Wagner, S. F. Altschul, S. M. Ulam, Satya N. Majumdar, Sergei Nechaev, V. Dancik   +14 more
core   +3 more sources

Mapping the evolution of mitochondrial complex I through structural variation

FEBS Letters, EarlyView.
Respiratory complex I (CI) is crucial for bioenergetic metabolism in many prokaryotes and eukaryotes. It is composed of a conserved set of core subunits and additional accessory subunits that vary depending on the organism. Here, we categorize CI subunits from available structures to map the evolution of CI across eukaryotes. Respiratory complex I (CI)
Dong‐Woo Shin, Tingting Chen, James A. Letts   +2 more
wiley   +1 more source

Hardware Accelerated Sequence Alignment with Traceback

International Journal of Reconfigurable Computing, 2009
Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner ...
Scott Lloyd, Quinn O. Snell
doaj   +1 more source

High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH

BMC Bioinformatics, 2010
Background Protein alignments are an essential tool for many bioinformatics analyses. While sequence alignments are accurate for proteins of high sequence similarity, they become unreliable as they approach the so-called 'twilight zone' where sequence ...
Bastolla Ugo, Minning Jonas, Teichert Florian, Porto Markus   +3 more
doaj   +1 more source

Higher accuracy protein Multiple Sequence Alignment by Stochastic Algorithm [PDF]

, 2010
Multiple Sequence Alignment gives insight into evolutionary, structural and functional relationships among the proteins. Here, a novel Protein Alignment by Stochastic Algorithm (PASA) is developed.
Alpana Dey, Justin Jose, Krishna Kant, M. S. Jeevitesh, Narayan Behera   +4 more
core   +1 more source

Topological network alignment uncovers biological function and phylogeny

, 2009
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact.
Cook S., Flannick J., Kuchaiev O., Kuchaiev O., Memišević V., Nataša Pržulj, Oleksii Kuchaiev, Pržulj N., Singh R., Singh R., Snijders T. A., Tijana Milenković, Vesna Memišević, Wayne Hayes, Wentz-Hunter K., Zhang Y.   +15 more
core   +2 more sources

Plasmodium falciparum gametogenesis essential protein 1 (GEP1) is a transmission‐blocking target

FEBS Letters, EarlyView.
This study shows Plasmodium falciparum GEP1 is vital for activating sexual stages of malarial parasites even independently of a mosquito factor. Knockout parasites completely fail gamete formation even when a phosphodiesterase inhibitor is added. Two single‐nucleotide polymorphisms (V241L and S263P) are found in 12%–20% of field samples.
Frederik Huppertz, Milagros Siebeck Caturelli, Lina S. Lehmann, Florian Kurth, Alexander G. Maier, Kai Matuschewski   +5 more
wiley   +1 more source