Predicting Thermophilic Proteins with Pseudo Amino Acid Composition:Approached from Chaos Game Representation and Principal Component Analysis

2011 ◽  
Vol 18 (12) ◽  
pp. 1244-1250 ◽  
Author(s):  
Xiao-Lei Liu ◽  
Jin-Long Lu ◽  
Xue-Hai Hu
Icarus ◽  
2003 ◽  
Vol 166 (2) ◽  
pp. 403-409 ◽  
Author(s):  
Evan D. Dorn ◽  
Gene D. McDonald ◽  
Michael C. Storrie-Lombardi ◽  
Kenneth H. Nealson

Foods ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 397 ◽  
Author(s):  
Dan Liu ◽  
Yu-Qing Chen ◽  
Xiao-Wei Xiao ◽  
Ru-Ting Zhong ◽  
Cheng-Feng Yang ◽  
...  

Many delicious and nutritional macrofungi are widely distributed and used in East Asian regions, considered as edible and medicinal foods. In this study, 11 species of dried and fresh, edible and medicinal macrofungi, Ganoderma amboinense, Agaricus subrufescens, Dictyophora indusiata, Pleurotus sajor-caju, Pleurotus ostreatus, Pleurotus geesteranu, Hericium erinaceus, Stropharia rugosoannulata, Pleurotus sapidus, Antrodia camphorata, and Lentinus edodes (Berk.) Sing, were investigated to determine the content of their nutritional components, including proteins, fat, carbohydrates, trace minerals, coarse cellulose, vitamins, and amino acids. The amino acid patterns and similarity of macrofungi were distinguished through principal component analysis and hierarchical cluster analyses, respectively. A total of 103 metabolic small molecules of macrofungi were identified by nuclear magnetic resonance spectroscopy and were aggregated by heatmap. Moreover, the macrofungi were classified by principal component analysis based on these metabolites. The results show that carbohydrates and proteins are two main components, as well as the nutritional ingredients, that differ among various species and varied between fresh and dried macrofungi. The amino acid patterns in L. edodes and A. subrufescens were different compared with that of the other tested mushrooms.


2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Bhagwan N. Rekadwad ◽  
Juan M. Gonzalez ◽  
Chandrahasya N. Khobragade

A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709–AM260713). Genome-to-Genome Distance (GGDC) showed high similarity to Pseudoalteromonas haloplanktis (X67024). The generated unique Quick Response (QR) codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR) showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR) indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates) using MEGA6 software. Principal Component Analysis (PCA) was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification.


1999 ◽  
Author(s):  
Joseph Vilain ◽  
Alain Giron ◽  
Djamel Brahmi ◽  
Patrick Deschavanne ◽  
Bernard Fertil

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