The statistical models that test alignments for significance make it possible to group sequences objectively, even when most or all of the interrelationships are weak. These tests are very sensitive, while remaining quite conservative, and discourage the addition of "misfit" sequences to an existing...
In light of how variable or conserved a region is, between two or more sequences, much can be said regarding the significance of the region for maintaining functional and structural integrity. Sequence alignment is also the first step in most of the bioinformatics analysis. Domains of high ...
Accuracy on multiple sequence alignments (MSA) is of great significance for such important biological applications as evolution and phylogenetic analysis, homology and domain structure prediction. In such analyses, alignment accuracy is crucial. In this paper, we investigate a combined scoring function ...
The alignment maximizes an alignment scoring function. The method is based on a novel extension of our consensus sequence methods. The algorithm works for both DNA and protein sequences, and from earlier work on consensus sequences, it is possible to estimate statistical significance. 关键词: PC...
Due to MSA significance, many MSA algorithms have been developed. Unfortunately, constructing accurate multiple sequence alignments is a computationally intense and biologically complex task, and as such, no current MSA tool is likely to generate a biologically perfect result. Therefore, this area of ...
andthedynamicprogrammingalgorithm.Theconceptsofsimilarity, significance,andhomologyarenextdiscussed.Theseprinciplesarethenextendedtomultiplesequence alignmentandanalysisanditsvariedapplications,specificallymotif,profile,andphylogenetictechniques.A briefdiscussionofmultiplesequencealignmentrelatedtoproteinstructurepredictionconcludes...
A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algo...
Motivation: Traditional alignment-based phylogenetic footprinting approaches make predictions on the basis of a single assumed alignment. The predictions a... R Satija,L Pachter,J Hein - 《Bioinformatics》 被引量: 61发表: 2008年 Pairwise statistical significance of local sequence alignment using multi...
Understanding of amino acid type co-occurrence in trusted multiple sequence alignments is a prerequisite for improved sequence alignment and remote homology detection algorithms. Two objective approaches were used to investigate co-occurrence, both based on variance maximization of the weighted residue frequ...
RNAcode -- Analyze the protein coding potential in multiple sequence alignments 0. About RNAcode === RNAcode predicts protein coding regions in an alignment of homologous nucleotide sequences. The prediction is based on evolutionary signatures typical for protein genese, i.e. the presence of synon...