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Why T-ACE

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).


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