EvoMS: An evolutionary tool to find de novo metabolic pathways

被引：4
|
作者：
Gerard, Matias F. [1 ]
Stegmayer, Georgina [1 ]
Milone, Diego H. [1 ]
机构：
[1] FICH UNL CONICET, Res Inst Signals Syst & Computat Intelligence Sin, Santa Fe, Argentina
来源：
BIOSYSTEMS | 2015年 / 134卷
关键词：
Evolutionary algorithms; Metabolic network representation; Metabolic pathway searching; Pathway synthesis; NETWORKS; KEGG;
D O I：
10.1016/j.biosystems.2015.04.006
中图分类号：
Q [生物科学];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
The evolutionary metabolic synthesizer (EvoMS) is an evolutionary tool capable of finding novel metabolic pathways linking several compounds through feasible reactions. It allows system biologists to explore different alternatives for relating specific metabolites, offering the possibility of indicating the initial compound or allowing the algorithm to automatically select it. Searching process can be followed graphically through several plots of the evolutionary process. Metabolic pathways found are displayed in a web browser as directed graphs. In all cases, solutions are networks of reactions that produce linear or branched metabolic pathways which are feasible from the specified set of available compounds. Source code of EvoMS is available at http://sourceforge.net/projects/sourcesinc/files/evoms/. Subsets of reactions are provided, as well as four examples for searching metabolic pathways among several compounds. Available as a web service at http://fich.unl.edu.ar/sinc/web-demo/evoms/. (C) 2015 Elsevier Ireland Ltd. All rights reserved.
引用
收藏
页码：43 / 47
页数：5
相关论文
共 50 条
  • [21] Long-term hypoxia exposure impairs metabolic pathways of de novo lipogenesis in young mouse adipocytes
    Slovakova, Lucie
    Pospisilova, Katerina
    Vavra, Jiri
    Polak, Jan
    PHYSIOLOGY, 2023, 38
  • [22] Transcriptome analysis of gall oak (Quercus infectoria): De novo assembly, functional annotation and metabolic pathways analysis
    Joudaki, Forough
    Ismaili, Ahmad
    Sohrabi, Seyed Sajad
    Hosseini, Seyedeh Zahra
    Kahrizi, Danial
    Ahmadi, Hadi
    GENOMICS, 2023, 115 (02)
  • [23] De novo lipogenesis in humans: metabolic and regulatory aspects
    Hellerstein, MK
    EUROPEAN JOURNAL OF CLINICAL NUTRITION, 1999, 53 (Suppl 1) : S53 - S65
  • [24] De novo experimental animal model of metabolic syndrome
    Lin, ShuGuang
    Huang, XiaoZhong
    Yu, XiYong
    Fei, HongWen
    Fu, YongHeng
    Liu, XiaoYing
    Wi, WeXang
    JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY, 2007, 42 : S61 - S62
  • [25] Advancing de novo lipogenesis: Genetic and metabolic insights
    Hartig, Sean M.
    Herman, Mark A.
    CELL METABOLISM, 2025, 37 (01) : 3 - 4
  • [26] De Novo Metabolic Engineering and the Promise of Synthetic DNA
    Klein-Marcuschamer, Daniel
    Yadav, Vikramaditya G.
    Ghaderi, Adel
    Stephanopoulos, Gregory N.
    BIOSYSTEMS ENGINEERING I: CREATING SUPERIOR BIOCATALYSTS, 2010, 120 : 101 - 131
  • [27] De novo lipogenesis in humans: metabolic and regulatory aspects
    MK Hellerstein
    European Journal of Clinical Nutrition, 1999, 53 : s53 - s65
  • [28] UniNovo: a universal tool for de novo peptide sequencing
    Jeong, Kyowon
    Kim, Sangtae
    Pevzner, Pavel A.
    BIOINFORMATICS, 2013, 29 (16) : 1953 - 1962
  • [29] Genes from scratch - the evolutionary fate of de novo genes
    Schloetterer, Christian
    TRENDS IN GENETICS, 2015, 31 (04) : 215 - 219
  • [30] AUDENS:: A tool for automated peptide de novo sequencing
    Grossmann, J
    Roos, FF
    Cieliebak, M
    Lipták, Z
    Mathis, LK
    Müller, M
    Gruissem, W
    Baginsky, S
    JOURNAL OF PROTEOME RESEARCH, 2005, 4 (05) : 1768 - 1774
12345