(most randomly-selected protein pairs are unrelated, but still might return an 'alignment'). Tree refinement - a computationally expensive procedure - ameliorates branch crumpling, but does not overcome left-right branch 'freeze-out' that may place potential neighbors on opposite sides of a ...
instead of something more self-explanatory like this? -# Note: unaligned sequences are provided as "aligned" sequences to avoid an initial full-DB alignment -# as we re-align everything after subsampling. inputs: - name: open metadata: "s3://nextstrain-data/files/ncov/open/metadata.tsv....
In this technique, we model the motion-based video temporal alignment problem as a spatio-temporal discrete trajectory point sets alignment problem. First, the trajectory of the object of interest is tracked throughout the videos. A probabilistic method is then developed to calculate the 'soft' ...
Public databases contain a planetary collection of nucleic acid sequences, but their systematic exploration has been inhibited by a lack of efficient methods for searching this corpus, which (at the time of writing) exceeds 20 petabases and is growing exponentially1. Here we developed a cloud com...
Some conceptual issues that arise in course of our investigation have been addressed. A few interesting problems related to the statistics of DNA words have been pointed out with some indication of their possible solutions. The work has been partially motivated by the fact that sequence alignment ...
The N-terminal 33 residues of the mature protein form a continuous stretch of high sequence conservation (48% average pairwise sequence identity) encompassing the region interacting with CsgG and forming the CsgF constriction peptide. CsgF homologues included in the multiple sequence alignment are ...
The contigs from the two new pig assemblies were aligned to the Sus scrofa 11.1 using minimap2 [35], and variants were identified using minimap2 module paftools.js based on the assembly-versus-assembly alignment. We annotated the variants using the Ensembl Variant Effect Predictor (VEP) build ...
Retain all primary mappings. Also retain up to-N[=5] top secondary mappings if their chaining scores are higher than-p[=0.8] of their corresponding primary mappings. If alignment is requested, filter out an internal seed if it potentially leads to both a long insertion and a long deletion....
https://github.com/mmagnus/rna-tools/blob/master/rna_tools/tools/rna_alignment/rna_alignment.ipynb References Components of rna-tools are based upon the following pieces of scientific literature: P. J. A. Cock, T. Antao, J. T. Chang, B. A. Chapman, C. J. Cox, A. Dalke, I. Frie...
we produced metaplots of ATAC-seq and H3K4me3 signals for TSSs in the syntheticHPRT1andHPRT1Rloci and throughout the yeast genome (Fig.2e,fand Extended Data Fig.4c). The metaplot profiles for the synthetic loci generally match that for the yeast genome and, although they lack the precise...