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EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms
Title
EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms
Author
Janies, Daniel, Witter, Zachary, Linchangco, Gregorio V., Jr.
Date Created
2016
Subjects--Topical
Genomics, Biology
Description
Background: One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation transcriptome data. The current dataset is the largest assembled for echin...
JED: a Java essential dynamics program for comparative analysis of protein trajectories
Title
JED: a Java essential dynamics program for comparative analysis of protein trajectories
Author
Jacobs, Donald J., Ramaprasad, Azhagiya Singam Ettayapuram, David, Charles C.
Date Created
2017
Subjects--Topical
Biology, Proteins
Description
Background: Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two common approaches to dete...
JEDi: Java essential dynamics inspector - a molecular trajectory analysis toolkit
Title
JEDi: Java essential dynamics inspector - a molecular trajectory analysis toolkit
Author
Jacobs, Donald J., Avery, Chris
Date Created
2021
Subjects--Topical
Biology, Proteins
Description
Background Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized soft...