The MCC values are 54, 60 and 41%, respectively, higher than that by the second best predictor FIEFDom, which is a homologous method-based on PSI-BLAST search.
Some of these interactions are redundant as they are obtained from different datasets, or predicted by homologous methods.
The sequencing data was assembled into nine megascaffolds based on 3 605 scaffolds, from which 26 685 protein coding genes consisting of 132 653 exons, 108 887 introns and 628 200 repetitive sequences were predicted using de novo and homologous methods with MAKER (version 2.22) (2.22
The M. notabilis genomic assembly is composed of 110 760 scaffolds, from which 27 085 protein-coding genes consisting of 124 550 exons, 81 rRNA genes, 560 tRNA genes, 311 snRNA genes, 233 microRNA genes and 324 736 repetitive sequences were predicted using de novo and homologous methods (Table 1).
To elucidate the possible role of S174 phosphorylation, we built a structural model of Saccharomyces cerevisiae Atg31 using a homologous modeling method and a threading modeling method (Pronk et al., 2013).
To characterize the in vivo functions of the predicted halogenase, the putative methyltransferase and the glycosyltransferases encoded by the vcm cluster, in-frame monogenic mutants of AORI_1485 (vhal), AORI_1490 (vmt), AORI_1486 (gtfD), and AORI_1487 (gtfE) are successfully constructed using a homologous recombination method similar to the PCR-targeting system (Methods).
DMP1-Tg mouse model was created with Gateway, a bacteriophage-based homologous recombination method by Cyagen Bioscience Inc. (Guangzhou, China).
S89G-DMP1 knock-in point mutation mouse model was created with homologous recombination method by Beijing Biocytogen Co., Ltd, China.
Epitope-tagging, promoter replacement and gene deletion were constructed by PCR-based homologous recombination method as described earlier (Longtine et al., 1998).
The tri11, tri3, and tri4 genes in the tri cluster of T. brevicompactum 0248 were deleted by homologous recombination method as previously described (Brown et al. 2004; Kumar 2010).
Gene disruption by homologous recombination method is not efficient in P. syringae.
