Benchmarking microbial growth rate predictions from metagenomes
نویسندگان
چکیده
منابع مشابه
Microbial goods from single cells and metagenomes.
Juan-Luis Ramos is a full-time professor of the CSIC and a member of the EC-US Task Force on Environmental Biotechnology. His main research interest is biodegradation from a wide perspective ranging from aspects of gene regulation to microbial ecology. All current environmental genomics studies are originated from Norm Pace’s cultivation-independent survey approach to study natural microbial po...
متن کاملDeciphering RNA structural diversity and systematic phylogeny from microbial metagenomes
Metagenomics has been employed to systematically sequence, classify, analyze and manipulate the entire genetic material isolated from environmental samples. Finding genes within metagenomic sequences remains a formidable challenge, and noncoding RNA genes other than those encoding rRNA and tRNA are not well annotated in metagenomic projects. In this work, we identify, validate and analyze the g...
متن کاملMicrobial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes.
Shotgun metagenomic sequencing does not depend on gene-targeted primers or PCR amplification; thus, it is not affected by primer bias or chimeras. However, searching rRNA genes from large shotgun Illumina data sets is computationally expensive, and no approach exists for unsupervised community analysis of small-subunit (SSU) rRNA gene fragments retrieved from shotgun data. We present a pipeline...
متن کاملStatic benchmarking of membrane helix predictions
Prediction of trans-membrane helices continues to be a difficult task with a few prediction methods clearly taking the lead; none of these is clearly best on all accounts. Recently, we have carefully set up protocols for benchmarking the most relevant aspects of prediction accuracy and have applied it to >30 prediction methods. Here, we present the extension of that analysis to the level of an ...
متن کاملExploration of community traits as ecological markers in microbial metagenomes.
The rate of information collection generated by metagenomics is uncoupled with its meaningful ecological interpretation. New analytical approaches based on functional trait-based ecology may help to bridge this gap and extend the trait approach to the community level in vast and complex environmental genetic data sets. Here, we explored a set of community traits that range from nucleotidic to g...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: The ISME Journal
سال: 2020
ISSN: 1751-7362,1751-7370
DOI: 10.1038/s41396-020-00773-1