Sentence examples for by reconstructing an alignment from inspiring English sources
BLASTX programs, although capable of insightful results thanks to the six frame translations, have the limitation of not being able to transparently manage frameshifts that occur inside the sequence, for example by reconstructing an alignment from pieces obtained on different reading frames.
A maximum likelihood (ML) phylogeny was reconstructed from an alignment of all the PR proteins.
Phylogenetic ages of splice sites were estimated from MULTIZ-46way alignments by reconstructing the ancestral sequence and dating the first occurrence of the splice site based on the ancestors of modern humans (Supplementary Note 1).
One possibility for reconstructing an overall consensus sequence is to find a minimum tiling path through haplotype assemblies, from the first base in the alignment to the last.
These guys demonstrated the technique numerically to reconstruct the shape of a poliovirus and also demonstrated it practically by reconstructing the 3-D shape shown above.
Reconstructing a single phylogenetic tree from a collection of individual genes by using concatenated alignments has long been common practice in phylogenetic analyses.
The main idea of MSARC is to reconstruct the alignment by clustering an alignment graph into columns.
If n1 is still big, we can use the standard technique in [ 12] to reduce the space to O(n1) by doubling the computation time for reconstructing the alignment of t.
In practice, however, the true MSA is not available and an MSA has to be reconstructed from the sequence data by an alignment program.
To evaluate the extent of DNA loss occurring in the olive genome because of unequal recombination between LTRs, we estimated the frequency of LTRs and inter-LTR regions by mapping the large Illumina read set onto a sample of 26 full-length LTR-retrotransposon sequences reconstructed by alignment of contigs belonging to single clusters obtained by graph-based clustering (Novák et al. 2010).
In addition, we generated an alignment using DIALIGN [ 37], which is a non-progressive alignment method, and subsequently reconstructed a PHYML-tree based on this alignment.
