Go Back   SEQanswers > Literature Watch

Similar Threads
Thread Thread Starter Forum Replies Last Post
Transcriptome reconstruction from RNA-seq data using Scripture. Joker!sAce Bioinformatics 13 12-06-2013 11:31 AM
RNA-seq: ab initio reconstruction of transcriptome with prokaryotes pasta RNA Sequencing 3 07-26-2011 07:22 PM
RNA-Seq: Computational methods for transcriptome annotation and quantification using Newsbot! Literature Watch 0 05-31-2011 02:40 AM
SAMMate 2.5 - Transcriptome quantification at the isoform-level using RNA-seq xuguorong Bioinformatics 0 04-08-2011 01:59 PM
RNA-Seq: Accurate quantification of transcriptome from RNA-Seq data by effective leng Newsbot! Literature Watch 0 11-10-2010 02:00 AM

Thread Tools
Old 12-04-2012, 02:00 AM   #1
RSS Posting Maniac

Join Date: Feb 2008
Posts: 1,443
Default RNA-Seq: Improved transcriptome quantification and reconstruction from RNA-Seq reads

Syndicated from PubMed RSS Feeds

Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations.

In Silico Biol. 2012 Jan 1;11(5):251-61

Authors: Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A

The paper addresses the problem of how to use RNA-Seq data for transcriptome reconstruction and quantification, as well as novel transcript discovery in partially annotated genomes. We present a novel annotation-guided general framework for transcriptome discovery, reconstruction and quantification in partially annotated genomes and compare it with existing annotation-guided and genome-guided transcriptome assembly methods. Our method, referred as Discovery and Reconstruction of Unannotated Transcripts (DRUT), can be used to enhance existing transcriptome assemblers, such as Cufflinks [3], as well as to accurately estimate the transcript frequencies. Empirical analysis on synthetic datasets confirms that Cufflinks enhanced by DRUT has superior quality of reconstruction and frequency estimation of transcripts.

PMID: 23202426 [PubMed - in process]

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 06:22 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO