Metagenome and Metatranscriptome Analyses Using Protein Family Profiles.

ABSTRACT: Analyses of metagenome data (MG) and metatranscriptome data (MT) are often challenged by a paucity of complete reference genome sequences and the uneven/low sequencing depth of the constituent organisms in the microbial community, which respectively limit the power of reference-based alignment and de novo sequence assembly. These limitations make accurate protein family classification and abundance estimation challenging, which in turn hamper downstream analyses such as abundance profiling of metabolic pathways, identification of differentially encoded/expressed genes, and de novo reconstruction of complete gene and protein sequences from the protein family of interest. The profile hidden Markov model (HMM) framework enables the construction of very useful probabilistic models for protein

SUBMITTER: Zhong C 

PROVIDER: S-EPMC4939949 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature