Go Back   SEQanswers > Literature Watch

Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: Jaguc - a software package for environmental diversity analyses. Newsbot! Literature Watch 0 11-16-2011 03:00 AM
sequencing of short DNA fragments (40-240bp) volks SOLiD 1 09-07-2010 06:04 AM
PubMed: Massively parallel display of genomic DNA fragments by rolling-circle amplifi Newsbot! Literature Watch 0 07-07-2010 11:20 AM
Short reads fragments of genome... hicham Bioinformatics 2 03-24-2010 05:15 AM
PubMed: Species detection using environmental DNA from water samples. Newsbot! Literature Watch 0 04-11-2008 09:11 AM

Thread Tools
Old 02-21-2008, 06:17 AM   #1
RSS Posting Maniac

Join Date: Feb 2008
Posts: 1,443
Default PubMed: Phylogenetic classification of short environmental DNA fragments.

Syndicated from PubMed RSS Feeds

Phylogenetic classification of short environmental DNA fragments.
Nucleic Acids Res. 2008 Feb 19;
Authors: Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J
Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives the opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, the phylogenetic analysis of the short reads produced represents a significant computational challenge. The phylogenetic algorithm CARMA for predicting the source organisms of environmental 454 reads is described. The algorithm searches for conserved Pfam domain and protein families in the unassembled reads of a sample. These gene fragments (environmental gene tags, EGTs), are classified into a higher-order taxonomy based on the reconstruction of a phylogenetic tree of each matching Pfam family. The method exhibits high accuracy for a wide range of taxonomic groups, and EGTs as short as 27 amino acids can be phylogenetically classified up to the rank of genus. The algorithm was applied in a comparative study of three aquatic microbial samples obtained by 454 pyrosequencing. Profound differences in the taxonomic composition of these samples could be clearly revealed.
PMID: 18285365 [PubMed - as supplied by publisher]

Newsbot! is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 10:25 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO