eBook: Megatenomics

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Microbiology ebook:

Name of book: Metagenomics

This publication contains a collection of chapters developed by NCBI from metagenome projects submitted to the Genomes Projects database. These chapters provide links to the sequence data and genome project submission as well as to BLAST, taxonomic lineages and publications.

Metagenomics is the functional and sequence-based analysis of the collective microbial genomes that are contained in an environmental sample. The word metagenomics describes “the notion of analysis of a collection of similar but not identical items, as in a meta-analysis, which is an analysis of analyses” (Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004 Dec;68(4):669-85.). Metadata from each metagenome project has been divided into the following categories for presentation within the Book Chapter:

WGS study Whole Genome Shotgun sequences that have been submitted for each metagenome project. WGS projects consist of contigs (and in some cases singletons) isolated from the described environmental source. See http://www.ncbi.nlm.nih.gov/Genbank/wgs.html for more information about WGS submissions.

Contig A non-redundant sequence formed by joining, based on sequence overlap, one or more smaller sequences. There should be no gaps.

Scaffold A non-redundant sequence formed by joining one or more contig sequences. A sequence overlap is not required to form a scaffold. Typically, a scaffold contains one or more gaps. The identification of genomes using WGS scaffolds is included within the Genome Assembly portion of the project summary.

Trace data Single-pass reads (including DNA sequence chromatograms, base calls, and quality estimates) submitted to the Trace Archive. See http://www.ncbi.nlm.nih.gov/Traces/trace.cgi for more information about the Trace Archive.

16S ribosomal RNA 16S ribosomal RNA sequences that have been submitted to GenBank. These may have been used in determining taxonomic phylotypes within the metagenome.

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