Results 21 to 30 of about 1,223,016 (311)

MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution [PDF]

, 2006
Background Non-coding DNA sequences comprise a very large proportion of the total genomic content of mammals, most other vertebrates, many invertebrates, and most plants. Unraveling the functional significance of non-coding DNA depends on how well we are
Johnson Toby, Wang Jun, Johnson, Toby, Keightley Peter D, Keightley, Peter, Wang, Jun   +5 more
core   +1 more source

transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences

BMC Bioinformatics, 2005
Background Alignments of homologous DNA sequences are crucial for comparative genomics and phylogenetic analysis. However, multiple alignment represents a computationally difficult problem.
Bininda-Emonds Olaf RP
doaj   +1 more source

The Secret Life of the Inhibitor of Virus Replication

Viruses, 2022
The inhibitor of virus replication (IVR) is an inducible protein that is not virus-target-specific and can be induced by several viruses. The GenBank was interrogated for sequences closely related to the tobacco IVR.
Peter Palukaitis, Masoud Akbarimotlagh, Eseul Baek, Ju-Yeon Yoon   +3 more
doaj   +1 more source

DNAssist, a C++ Program for Editing and Analysis of Nucleic Acid and Protein Sequences on PC-Compatible Computers Running Windows 95, 98, NT4.0 or 2000

BioTechniques, 2000
The size of sequence databases, the rapid rate of generating sequence data and the need to routinely construct recombinant DNA molecules in molecular biological research necessitate the frequent handling and analysis of nucleotide and protein sequences ...
Hugh G. Patterton, Steven Graves
doaj   +1 more source

Genome-scale DNA sequence data and the evolutionary history of placental mammals

Data in Brief, 2018
We present a genomic data set comprised of the coding DNA sequences of 5162 loci from 90 vertebrate species, including 82 mammals. The loci were aligned with their protein sequences.
Shaoyuan Wu, Scott Edwards, Liang Liu
doaj   +1 more source

FramePlus: aligning DNA to protein sequences

Bioinformatics, 1999
Abstract Motivation: Automated annotation of Expressed Sequence Tags (ESTs) is becoming increasingly important as EST databases continue to grow rapidly. A common approach to annotation is to align the gene fragments against well-documented databases of protein sequences.
Eran Halperin, Simchon Faigler, Raveh Gill-More   +2 more
openaire   +2 more sources

An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs [PDF]

, 2010
Background: Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biology and includes the subtask of ...
García Alcalde, Fernando, Blanco Morón, Armando, Armando Blanco, Blanco, A., Blanco Armando, Shepherd Adrian J, Shepherd, Adrian J., Garcia-Alcalde Fernando, Garcia-Alcalde, F., Adrian J Shepherd, Fernando Garcia-Alcalde   +10 more
core   +1 more source

Frequent Patterns Mining in DNA Sequence

IEEE Access, 2019
As a common biological sequence, DNA sequences contain important information. The discovery of frequent patterns in DNA sequences can help to study the evolution, function and variation of genes.
Na Deng, Xu Chen, Desheng Li, Caiquan Xiong   +3 more
doaj   +1 more source

A Multimodal Approach towards Genomic Identification of Protein Inhibitors of Uracil-DNA Glycosylase

Viruses, 2023
DNA-mimicking proteins encoded by viruses can modulate processes such as innate cellular immunity. An example is Ung-family uracil-DNA glycosylase inhibition, which prevents Ung-mediated degradation via the stoichiometric protein blockade of the Ung DNA ...
Wael Muselmani, Naail Kashif-Khan, Claire Bagnéris, Rosalia Santangelo, Mark A. Williams, Renos Savva   +5 more
doaj   +1 more source

Benchmarking tools for the alignment of functional noncoding DNA [PDF]

, 2004
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics. 2004;5(1): 6.Background: Numerous tools have been developed to align genomic sequences.
Celniker SE, Eisen MB, MB Eisen, Stoye J, Bergman CM, Celniker, Susan E., Bergman, Casey M., SE Celniker, Pollard, Daniel A., Pollard DA, CM Bergman, Eisen, Michael B., J Stoye, Stoye, Jens, Stoye, Jens ; https://orcid.org/, DA Pollard   +15 more
core   +2 more sources