Zobrazeno 1 - 10
of 12
pro vyhledávání: '"Gregory E. Sims"'
Publikováno v:
PLoS ONE, Vol 7, Iss 10, p e46688 (2012)
As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of
Externí odkaz:
https://doaj.org/article/c2ceb4a084d04415961af97935940f5d
Autor:
Christopher D. Town, Kathryn V. Holmes, Christine C. Robinson, David E. Wentworth, Gregory E. Sims, Samuel R. Dominguez, Rebecca A. Halpin
Publikováno v:
Journal of General Virology
This study compared the complete genome sequences of 16 NL63 strain human coronaviruses (hCoVs) from respiratory specimens of paediatric patients with respiratory disease in Colorado, USA, and characterized the epidemiology and clinical characteristi
Autor:
Sung-Hou Kim, Gregory E. Sims
Publikováno v:
Proceedings of the National Academy of Sciences. 108:8329-8334
A whole-genome phylogeny of the Escherichia coli / Shigella group was constructed by using the feature frequency profile (FFP) method. This alignment-free approach uses the frequencies of l -mer features of whole genomes to infer phylogenic distances
Publikováno v:
Proceedings of the National Academy of Sciences
The vast sequence divergence among different virus groups has presented a great challenge to alignment-based sequence comparison among different virus families. Using an alignment-free comparison method, we construct the whole-proteome phylogeny for
Autor:
Sung-Hou Kim, Gregory E. Sims
Publikováno v:
Proceedings of the National Academy of Sciences. 103:4428-4432
A method is presented for scoring the model quality of experimental and theoretical protein structures. The structural model to be evaluated is dissected into small fragments via a sliding window, where each fragment is represented by a vector of mul
Publikováno v:
Proceedings of the National Academy of Sciences. 102:618-621
We have mapped protein conformational space from two to seven residue lengths by employing multidimensional scaling on a data matrix composed of pair-wise angular distances for multiple ϕ-Ψ values collected from high-resolution protein structures.
Publikováno v:
Proceedings of the National Academy of Sciences. 100:2386-2390
One of the principal goals of the structural genomics initiative is to identify the total repertoire of protein folds and obtain a global view of the “protein structure universe.” Here, we present a 3D map of the protein fold space in which struc
We present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (FFPs) of whole proteomes. Features are l -mers of amino acids, and each organism is represented by a profile of frequencies of all features. The
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::01658fb1d7bc2667916caeab065c7672
https://europepmc.org/articles/PMC2806744/
https://europepmc.org/articles/PMC2806744/
Ten complete mammalian genome sequences were compared by using the “feature frequency profile” (FFP) method of alignment-free comparison. This comparison technique reveals that the whole nongenic portion of mammalian genomes contains evolutionary
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7ea0611f5d020a7fc166bb2b224fd01c
https://europepmc.org/articles/PMC2761373/
https://europepmc.org/articles/PMC2761373/
For comparison of whole-genome (genic + nongenic) sequences, multiple sequence alignment of a few selected genes is not appropriate. One approach is to use an alignment-free method in which feature (or l -mer) frequency profiles (FFP) of whole genome
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8cc27b3fccb9fedb1b853b7c4010580d
https://europepmc.org/articles/PMC2634796/
https://europepmc.org/articles/PMC2634796/