Next generation sequencing (NGS) technologies allow a rapid and cost-effective accumulation of
large RNA sequence data sets in model and non-model organisms. However the subsequent handling
of sequence information from different NGS platforms is still a significant bottleneck, leading to a
delay in data processing. We present here the Transcriptome Analysis and Comparison Explorer (T-ACE); a tool designed for the organization and analysis of large sequence datasets, and especially
suited for non-model organisms lacking genome information. T-ACE offers a TCL based database
interface, which accesses a PostgreSQL database via a php-script. Within T-ACE, information
belonging to a single sequence or contig, such as annotation or read coverage, is linked to the
respective sequence and immediately accessible. Sequences and assigned information can be
searched via keyword- or BLAST search, and whole transcriptomes analyzed on the level of
expression, GO terms, KEGG pathways and protein domains. Results are visualized and can be easily
exported for external analysis or further graphical processing. We developed T-ACE for laboratory
environments which have only a limited amount of bioinformatic support, and cooperation-projects
in which different partners work on the same dataset from different locations or platforms
(Windows/Linux/MacOS).
Have also in mind that T-ACE is not designed as a genome browser, but for de-novo transcriptomes.
This means, in the current state of T-ACE, contig sequences should not be much longer than 60.000
bp and should not contain over 100.000 reads (at least if those reads shall be displayed).