Quantitative assessment of protein function prediction from metagenomics shotgun sequences
نویسندگان
چکیده
منابع مشابه
Quantitative assessment of protein function prediction from metagenomics shotgun sequences.
To assess the potential of protein function prediction in environmental genomics data, we analyzed shotgun sequences from four diverse and complex habitats. Using homology searches as well as customized gene neighborhood methods that incorporate intergenic and evolutionary distances, we inferred specific functions for 76% of the 1.4 million predicted ORFs in these samples (83% when nonspecific ...
متن کاملBioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
One of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome...
متن کاملPrediction of disulfide connectivity from protein sequences.
The difficulties in predicting disulfide connectivity from protein sequences lie in the nonlocal properties of the disulfide bridges that involve cysteine pairs at large sequence separation. Though some progress has been recently made in the prediction of disulfide connectivity, the current methods predict less than half of the disulfide patterns for the data set sharing less than 30% sequence ...
متن کاملCharacterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
The advent of next generation sequencing (NGS) has enabled investigations of the gut microbiome with unprecedented resolution and throughput. This has stimulated the development of sophisticated bioinformatics tools to analyze the massive amounts of data generated. Researchers therefore need a clear understanding of the key concepts required for the design, execution and interpretation of NGS e...
متن کاملRecovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics
Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical material. We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a Brucella melitensis genome. Sequence reads from this 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: Proceedings of the National Academy of Sciences
سال: 2007
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.0702636104