Results 91 to 100 of about 4,988,216 (324)

MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts

BMC Bioinformatics, 2011
Background Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif ...
Deng Xin, Cheng Jianlin
doaj   +1 more source

Homology-extended sequence alignment [PDF]

Nucleic Acids Research, 2005
We present a profile-profile multiple alignment strategy that uses database searching to collect homologues for each sequence in a given set, in order to enrich their available evolutionary information for the alignment. For each of the alignment sequences, the putative homologous sequences that score above a pre-defined threshold are incorporated into
Simossis, V. A., Kleinjung, J., Heringa, J.   +2 more
openaire   +2 more sources

Calpain small subunit homodimerization is robust and calcium‐independent

FEBS Letters, EarlyView.
Calpains dimerize via penta‐EF‐hand (PEF) domains. Using single‐molecule force spectroscopy, we measured the strength and kinetics of PEF–PEF homodimer binding. The interaction is robust, shows a transient conformational step before dissociation, and remains largely insensitive to Ca2+.
Nesha May O. Andoy, Trina Dykstra‐MacPherson, Mathias A. Bell, Peter L. Davies, Ruby May A. Sullan   +4 more
wiley   +1 more source

Fine-tuning structural RNA alignments in the twilight zone

BMC Bioinformatics, 2010
Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance.
Schirmer Stefanie, Bremges Andreas, Giegerich Robert   +2 more
doaj   +1 more source

Scaling Laws and Similarity Detection in Sequence Alignment with Gaps [PDF]

, 1998
We study the problem of similarity detection by sequence alignment with gaps, using a recently established theoretical framework based on the morphology of alignment paths.
Drasdo, Dirk, Hwa, Terence, Lassig, Michael   +2 more
core   +3 more sources

SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation

PLoS ONE, 2014
The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that
Brejnev Muhire, A. Varsani, D. Martin
semanticscholar   +1 more source

Protein Multiple Sequence Alignment [PDF]

, 2008
Protein sequence alignment is the task of identifying evolutionarily or structurally related positions in a collection of amino acid sequences. Although the protein alignment problem has been studied for several decades, many recent studies have demonstrated considerable progress in improving the accuracy or scalability of multiple and pairwise ...
Chuong B, Do, Kazutaka, Katoh
openaire   +2 more sources

A methionine‐lined active site governs carbocation stabilization and product specificity in a bacterial terpene synthase

FEBS Letters, EarlyView.
This study reveals a unique active site enriched in methionine residues and demonstrates that these residues play a critical role by stabilizing carbocation intermediates through novel sulfur–cation interactions. Structure‐guided mutagenesis further revealed variants with significantly altered product profiles, enhancing pseudopterosin formation. These
Marion Ringel, Carl P. O. Helmer, Shani Zev, Ronja Driller, Emily Buhr, Markus Reinbold, Renana Schwartz, Gabriel Foley, Mikael Boden, Daniel Garbe, Gerhard Schenk, Dan Thomas Major, Bernhard Loll, Thomas Brück   +13 more
wiley   +1 more source

Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences

Algorithms
The standard approach for constructing a phylogenetic tree from a set of sequences consists of two key stages. First, a multiple sequence alignment (MSA) of the sequences is computed.
Mahbubeh Askari Rad, Alibek Kruglikov, Xuhua Xia   +2 more
doaj   +1 more source

MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data

BMC Bioinformatics, 2010
Background Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods.
Kryukov Kirill, Saitou Naruya
doaj   +1 more source