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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 Pearson, Webb Miller
exaly +4 more sources
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, J W Fickett
exaly +5 more sources
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies
Systematic Biology, 2023 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. Here, we
P. Kapli +4 more
semanticscholar +6 more sources
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
doaj +2 more sources
The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. [PDF]
BioTechniques, 2000 JavaScript is an object-based scripting language that can be interpreted by most commonly used Web browsers, including Netscape® Navigator® and Internet Explorer®.
P. Stothard
semanticscholar +5 more sources
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
doaj +2 more sources
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 +2 more sources
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.
C Sansom
exaly +3 more sources
Accelign: a GPU-based library for accelerating pairwise sequence alignment [PDF]
BMC BioinformaticsBackground The continually increasing volume of sequence data results in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments based on dynamic programming is an important part in many bioinformatics pipelines ...
Felix Kallenborn +3 more
doaj +2 more sources