Castillo2016 - Whole-genome metabolic model of C.neoformans using CoReCo

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. and Arvas, M. (2014). Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. PLoS Computational Biology, 10(2), e1003465. doi:10.1371/journal.pcbi.1003465 and Castillo, S., Barth, D., Arvas, M., Pakula, TM., Pitkanen, E., Blomberg, P., Penttila M., Oja M. Whole genome metabolic model of Trichoderma reesei built by comparative reconstruction.
CoReCo annotates each reaction with the following attributes:

reco:balanced: True, if reaction is in stoichiometric balance.
reco:posterior: CoReCo phase II probability
reco:cost: CoReCo phase II log-score
reco:level: High, if cost below reconstruction threshold, and Low, if cost above reconstruction threshold. A reaction with level=Low only appears in reconstruction to gapfill a reaction with level=High.
reco:naivep: CoReCo phase I probability.
reco:btscore: CoReCo phase II probability considering only BLAST as input.
reco:gtscore: CoReCo phase II probability considering only GTG as input.
reco:bscore: CoReCo BLAST score
reco:bseq1: Protein sequence in target species with highest BLAST score
reco:bseq2: Protein sequence in UniProt with highest BLAST score
reco:gscore: CoReCo GTG score
reco:gseq1: Protein sequence in target species
reco:gseq2: Protein sequence in GTG database with highest GTG score

本模型基于蛋白质序列与系统发育数据，采用CoReCo方法重构得到。CoReCo的相关方法详见以下两篇文献：
Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. 及 Arvas, M. (2014). 面向现存与祖先物种的无间隙代谢网络比较基因组规模重构. PLoS计算生物学, 10(2), e1003465. DOI:10.1371/journal.pcbi.1003465；
Castillo, S., Barth, D., Arvas, M., Pakula, T.M., Pitkanen, E., Blomberg, P., Penttila, M., Oja, M. 基于比较重构构建的里氏木霉全基因组代谢模型。

CoReCo可为每条代谢反应注释如下属性：
`reco:balanced`：若代谢反应符合化学计量平衡，则取值为True；
`reco:posterior`：CoReCo第二阶段的后验概率；
`reco:cost`：CoReCo第二阶段的对数得分；
`reco:level`：当反应的cost值低于重构阈值时标注为High，高于阈值时标注为Low。仅Level为Low的反应会在重构流程中用于填补Level为High的反应的间隙；
`reco:naivep`：CoReCo第一阶段的概率；
`reco:btscore`：仅以BLAST（Basic Local Alignment Search Tool，基本局部比对搜索工具）作为输入特征时，CoReCo第二阶段的后验概率；
`reco:gtscore`：仅以GTG作为输入特征时，CoReCo第二阶段的后验概率；
`reco:bscore`：CoReCo的BLAST得分；
`reco:bseq1`：靶标物种中BLAST得分最高的蛋白质序列；
`reco:bseq2`：UniProt（通用蛋白质资源数据库）中BLAST得分最高的蛋白质序列；
`reco:gscore`：CoReCo的GTG得分；
`reco:gseq1`：靶标物种中的蛋白质序列；
`reco:gseq2`：GTG数据库中GTG得分最高的蛋白质序列。