Go Back   SEQanswers > Applications Forums > Metagenomics

Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: Profiling of Short RNAs Using Helicos Single-Molecule Sequencing. Newsbot! Literature Watch 0 12-07-2011 04:10 AM
PubMed: Systematic artifacts in metagenomes from complex microbial communities. Newsbot! Literature Watch 0 07-10-2009 06:00 AM
PubMed: Metagenomic signatures of 86 microbial and viral metagenomes. Newsbot! Metagenomics 0 03-24-2009 06:00 AM
Second SOLiD Publication: Stem cell transcriptome profiling ECO SOLiD 0 06-03-2008 09:29 AM

Thread Tools
Old 01-13-2009, 06:04 AM   #1
RSS Posting Maniac

Join Date: Feb 2008
Posts: 1,443
Default PubMed: Profiling model T cell metagenomes with short reads.

Syndicated from PubMed RSS Feeds

Related Articles Profiling model T cell metagenomes with short reads.

Bioinformatics. 2009 Jan 9;

Authors: Warren RL, Nelson BH, Holt RA

MOTIVATION: T cell receptor (TCR) diversity in peripheral blood has not yet been fully profiled with sequence level resolution. Each T cell clonotype expresses a unique receptor, generated by somatic recombination of TCR genes and the enormous potential for T cell diversity makes repertoire analysis challenging. We developed a sequencing approach and assembly software (immuno-SSAKE or iSSAKE) for profiling T cell metagenomes using short reads from the massively parallel sequencing platforms. RESULTS: Models of sequence diversity for the TCR beta-chain CDR3 region were built using empirical data and used to simulate, at random, distinct TCR clonotypes at 1-20 parts per million. Using simulated TCRbeta (sTCRbeta) sequences, we randomly created 20 million 36nt reads having 1%-2% random error, 20 million 42nt or 50nt reads having 1% random error and 20 million 36nt reads with 1% error modeled on real short read data. Reads aligning to the end of known TCR variable (V) genes and having consecutive unmatched bases in the adjacent CDR3 were used to seed iSSAKE de novo assemblies of CDR3. With assembled 36nt reads we detect over 51% and 63% of rare (1 ppm) clonotypes using a random or modeled error distribution, respectively. We detect over 99% of more abundant clonotypes (6 ppm or higher) using either error distribution. Longer reads improve sensitivity, with assembled 42nt and 50nt reads identifying 82.0% and 94.7% of rare 1 ppm clonotypes, respectively. Our approach illustrates the feasibility of complete profiling of the TCR repertoire using new massively parallel short read sequencing technology. AVAILABILITY: CONTACT: SUPPLEMENTARY INFORMATION: Supplementary methods and data available at Bioinformatics online and at

PMID: 19136549 [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 11:58 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO