Results 1 to 10 of about 1,706,932 (293)
transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences [PDF]
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
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Database searching with DNA and protein sequences: An introduction [PDF]
Briefings in Bioinformatics, 2000 This review of sequence database searching aims to set out current practice in the area, in order to give practical guidelines to the experimental biologist. It describes the basic principles behind the programs and enumerates the range of databases available in the public domain.
Clare Sansom
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Journal of Integrative Bioinformatics, 2019 The interconversion of sequences that constitute the genome and the proteome is becoming increasingly important due to the generation of large amounts of DNA sequence data. Following mapping of DNA segments to the genome, one fundamentally important task
Li Yaoyong +2 more
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Comparison of DNA Sequences with Protein Sequences
Genomics, 1997 The FASTA package of sequence comparison programs has been expanded to include FASTX and FASTY, which compare a DNA sequence to a protein sequence database, translating the DNA sequence in three frames and aligning the translated DNA sequence to each sequence in the protein database, allowing gaps and frameshifts.
William R Pearson, Webb Miller
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Recognition of protein coding regions in DNA sequences
Nucleic Acids Research, 1982 We give a test for protein coding regions which is based on simple and universal differences between protein-coding and noncoding DNA. The test is simple enough to use without a computer and is completely objective. The test has been thoroughly proven on 400,000 bases of sequence data: it misclassifies 5% of the regions tested and gives an answer of ...
James W Fickett
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DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies
Systematic Biology, 2023 Abstract Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences.
Kapli, Paschalia +4 more
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Extended many-item similarity indices for sets of nucleotide and protein sequences
Computational and Structural Biotechnology Journal, 2021 Quantification of similarities between protein sequences or DNA/RNA strands is a (sub-)task that is ubiquitously present in bioinformatics workflows, and is usually accomplished by pairwise comparisons of sequences, utilizing simple (e.g.
Dávid Bajusz +3 more
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Two Dimensional Yau-Hausdorff Distance with Applications on Comparison of DNA and Protein Sequences. [PDF]
PLoS ONE, 2015 Comparing DNA or protein sequences plays an important role in the functional analysis of genomes. Despite many methods available for sequences comparison, few methods retain the information content of sequences.
Kun Tian +5 more
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More-SPEED: Enhancing Protein Activity Prediction from DNA Sequences
Iraqi Journal for Computer Science and Mathematics, 2023 This work presents More-SPEED, a novel model for accurately predicting protein activity while minimizing computational demands. Leveraging optimized structures and data preprocessing techniques, More-SPEED achieves high accuracy in protein activity ...
Samaher Al-Janabi, Zena A. Kadhuim
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Methods for comparing a DNA sequence with a protein sequence [PDF]
Bioinformatics, 1996 We describe two methods for constructing an optimal global alignment of, and an optimal local alignment between, a DNA sequence and a protein sequence. The alignment model of the methods addresses the problems of frameshifts and introns in the DNA sequence. The methods require computer memory proportional to the sequence lengths, so they can rigorously
Huang, Xiaoqiu, Zhang, Jinghui
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