Results 71 to 80 of about 1,259,867 (328)

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
Jaap Heringa, Jens Kleinjung, V. A. Simossis   +2 more
openaire   +3 more sources

Global Network Alignment [PDF]

, 2010
Motivation: High-throughput methods for detecting molecular interactions have lead to a plethora of biological network data with much more yet to come, stimulating the development of techniques for biological network alignment.
Natasa Przulj, Oleksii Kuchaiev
core   +1 more source

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

Generalized Sequence Alignment and Duality

Advances in Applied Mathematics, 1993
The problem of finding a longest common subsequence of two sequences \(s_ 1\), \(s_ 2, \dots, s_ n\) and \(t_ 1\), \(t_ 2, \dots, t_ m\) (LCS-problem) can be characterized within the theory of posets by studying a partial order on \(\{1,2, \dots, n\} \times \{1,2, \dots,m\}\) that is defined by means of a \(2 \times 2\)-matrix \(A\) over 0 and 1.
Pavel A. Pevzner, Michael S. Waterman
openaire   +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

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

A two-base encoded DNA sequence alignment problem in computational biology [PDF]

, 2009
The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics.
Chang, Jen-Mei, Drakes, Chiaka, Huang, Erya, Langat, Deidrey, McGrath, Joseph, Morabito, Mark, Pacheco, Jose, Rodriguez, Nancy, Salazar, Daniel, Vemuri, Rao, Vu, Man, Wadhar, Hem, Wu, Qin   +12 more
core  

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

Iterative refinement of structure-based sequence alignments by Seed Extension

BMC Bioinformatics, 2009
Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone.
Lee Byungkook, Tai Chin-Hsien, Kim Changhoon   +2 more
doaj   +1 more source

Sequence alignment generation using intermediate sequence search for homology modeling

Computational and Structural Biotechnology Journal, 2020
Protein tertiary structure is important information in various areas of biological research, however, the experimental cost associated with structure determination is high, and computational prediction methods have been developed to facilitate a more ...
Shuichiro Makigaki, Takashi Ishida
doaj   +1 more source