You do not have permission to edit this page, for the following reason:
The action you have requested is limited to users in the group: Users.
Short description:
Please summarise the application in a few sentences. Avoid links here. We introduce a clustering method which significantly reduces the size of a metagenome dataset while maintaining a faithful representation of its functional and taxonomic content.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Metagenomics,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Read mapping, Annotation,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
A typical metagenome dataset generated using a 454 pyrosequencing platform consists of short reads sampled from the collective genome of a microbial community. The amount of sequence in such datasets is usually insufficient for assembly, and traditional gene prediction cannot be applied to unassembled short reads. As a result, analysis of such datasets usually involves comparisons in terms of relative abundances of various protein families. The latter requires assignment of individual reads to protein families, which is hindered by the fact that short reads contain only a fragment, usually small, of a protein. We have considered the assignment of pyrosequencing reads to protein families directly using RPS-BLAST against COG and Pfam databases and indirectly via proxygenes that are identified using BLASTx searches against protein sequence databases. Using simulated metagenome datasets as benchmarks, we show that the proxygene method is more accurate than the direct assignment. We introduce a clustering method which significantly reduces the size of a metagenome dataset while maintaining a faithful representation of its functional and taxonomic content.
Once you save the form, you will have the chance to add links and references.
Summary of edit
This is a minor edit Watch this page
Cancel