منابع مشابه
compariSeq: Rethinking Sequence Logos
Comparing Sequence Charts (compariSeq) is a redesign of traditional sequence logos for the task of comparing multiple biological sequences. All relevant data encoded in traditional sequence logos is conserved, however, attention is directed to the most important data, colors are more perceptually accessible, and the task of direct comparison at particular locations is supported.
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The need to measure sequence similarity arises in many applicitation domains and often coincides with sequence alignment: the more similar two sequences are, the better they can be aligned. Aligning sequences not only shows how similar sequences are, it also shows where there are differences and correspondences between the sequences. Traditionally, the alignment has been considered for sequence...
متن کاملThe Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment
Most pairwise and multiple sequence alignment programs seek alignments with optimal scores. Central to defining such scores is selecting a set of substitution scores for aligned amino acids or nucleotides. For local pairwise alignment, substitution scores are implicitly of log-odds form. We now extend the log-odds formalism to multiple alignments, using Bayesian methods to construct "BILD" ("Ba...
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The objective of this work is to introduce a new method called the Survivorship Instantaneous Log-odds Ratios (SILOR); to illustrate the creation of SILOR from empirical bivariate survival functions; to also derive standard errors of estimation; to compare results with those derived from logistic regression. Hip fracture, AGE and BMI from the Third National Health and Nutritional Examination Su...
متن کاملSequence logos: a new way to display consensus sequences.
A graphical method is presented for displaying the patterns in a set of aligned sequences. The characters representing the sequence are stacked on top of each other for each position in the aligned sequences. The height of each letter is made proportional to its frequency, and the letters are sorted so the most common one is on top. The height of the entire stack is then adjusted to signify the...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2014
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btu634