GenDBE

GenDBE enables annotation and assembly of eukaryotic genomes and transcriptomes, supporting intron–exon gene models and integration of Roche/454 and Illumina sequencing data for transcript reconstruction and analysis.

Key Features:

• Eukaryotic gene model support: Handles intron and exon gene structures for eukaryotic genome annotation.
• Transcriptome integration with SAMS: Integrates with SAMS for eukaryotic transcriptome data representation and analysis.
• High-quality transcript assembly: Implements both de novo and reference-based strategies to reconstruct transcripts.
• Sequencing technology support: Accepts and leverages data from Roche/454 and Illumina platforms.
• Assembly toolchain: Employs Trinity and Oases for de novo assembly, ESTScan for CDS screening, cd-hit-est for redundancy filtering, CAP3 for re-assembly, and TopHat/Cufflinks, GMAP, and cuffmerge for reference-based assembly and merging.

Scientific Applications:

• CHO cell line transcriptomics: Enables assembly and analysis of Chinese hamster ovary (CHO) cell transcriptomes to support research on therapeutic protein production and optimization of protein expression.

Methodology:

De novo assembly using Trinity and Oases with varying k-mer sizes; screening of contigs for coding sequences with ESTScan; redundancy removal with cd-hit-est; re-assembly of CDS contigs with CAP3; reference-based assembly using the TopHat/Cufflinks pipeline against the CHO-K1 draft genome; mapping de novo contigs to the reference with GMAP and merging assemblies with cuffmerge.