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A novel DNAseq program for enhanced analysis of Illumina GAII data: a case study on antibody complementarity-determining regions

Paper ID Volume ID Publish Year Pages File Format Full-Text
33382 44976 2012 8 PDF Available
Title
A novel DNAseq program for enhanced analysis of Illumina GAII data: a case study on antibody complementarity-determining regions
Abstract

High-throughput DNA sequencing technologies are increasingly becoming powerful systems for the comprehensive analysis of variations in whole genomes or various DNA libraries. As they are capable of producing massive collections of short sequences with varying lengths, a major challenge is how to turn these reads into biologically meaningful information. The first stage is to assemble the short reads into longer sequences through an in silico process. However, currently available software/programs allow only the assembly of abundant sequences, which apparently results in the loss of highly variable (or rare) sequences or creates artefact assemblies. In this paper, we describe a novel program (DNAseq) that is capable of assembling highly variable sequences and displaying them directly for phylogenetic analysis. In addition, this program is Microsoft Windows-based and runs by a normal PC with 700 MB RAM for a general use. We have applied it to analyse a human naive single-chain antibody (scFv) library, comprehensively revealing the diversity of antibody variable complementarity-determining regions (CDRs) and their families. Although only a scFv library was exemplified here, we envisage that this program could be applicable to other genome libraries.

► Short read assembler for Illumina GAII data maximizing diversity description of a naive human antibody DNA-library. ► A new way of idiotype profiling: Phylogenetic analysis of the 6 antibody CDRs in the human naive library. ► A new computational assembling methodology based merely on overlapping sequences, increases assembly speed and optimize diversity description.

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A novel DNAseq program for enhanced analysis of Illumina GAII data: a case study on antibody complementarity-determining regions
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Publisher
Database: Elsevier - ScienceDirect
Journal: New Biotechnology - Volume 29, Issue 3, 15 February 2012, Pages 271–278
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us