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TSSAR: Transcription Start Site Annotation Regime Web Service

The TSSAR Web Server is the second major component in the TSSAR Web Service pipeline. It is responsible for scheduling and executing TSSAR jobs on TBI's hardware infrastructure by applying the TSSAR statistical model to data sets received by the TSSAR Client and provides convenient long-term access to computational results.

Introduction to the TSSAR Web Server

The TSSAR Web Server acts as superglue for the TSSAR pipeline. Based on a RESTful Web architecture, it connects the TSSAR Client with the underlying statistical model and provides access to result data. Upon data pre-processing and submission by the TSSAR Client, a confirmation email is sent to the user (if a contact email address has been provided). This email contains both the submission ID as well as a persistent URI for the computational results. This URI is also displayed in the TSSAR Client upon data submission.

This URI has the form http://nibiru.tbi.univie.ac.at/TSSAR/tss/data/<ID>, where <ID> is a unique identifier for your submission. Please note that it is essentially important to bookmark the TSSAR results URI since it links to the resource that contains all computational results of your TSSAR submission and cannot be retrieved later. In other words, if you loose the TSSAR results URI, you will not be able to view any results for your TSSAR submission in the browser.

Internally, the data is scheduled for processing on TBI's server infrastructure and the server-side computation (TSSAR statistics and post-processing) is started. Depending on the genome size of the organism provided and TBI's current server load, a TSSAR job typically takes several hours for completion. Once all computational tasks are done, a notification email is sent to the user, indicating the results URI again.

Post-Processing

Besides assessing every position in the genome for significant enrichment in the treated library, the TSSAR Web service provides additional functionality for post-processing analysis. Most importantly, TSSAR filters positions which fulfill user specified parameters (i.e. P-value and noise background) and makes them available in different file formats. Furthermore it is possible to merge consecutive putative TSS positions into the most prominent signal.

If a corresponding gene annotation has been provided, the annotated TSS list is related to its genomic context. Each annotated position is classified as Internal (I, within an annotated gene), Antisense (A, positioned directly antisense to an annotated gene; Ad, positioned antisense to the downstream region [max. 30 nt] of an annotated gene, thus very likely that the transcription from this TSS runs into the 3' part of the corresponding gene) or Primary TSS (P, max. 250 nt upstream of an annotated gene). Any combination of A, I and P is possible and illustrated in a Venn diagram. If a TSS does not match one of the above criteria, it is classified as Orphan (O).

From all TSS which are classified as Primary, the length of the untranslated region (5' UTR) can be deduced. The UTR length distribution is provided for each TSS annotation. All plots and the classification itself can be downloaded from the result page.

If TSSAR is useful for your work or if you use any figures or data procuced by TSSAR, please cite the original TSSAR publication: "TSSAR: TSS Annotation Regime for dRNA-seq data" F. Amman, M.T. Wolfinger, R. Lorenz, I.L. Hofacker, P.F. Stadler and S. Findeiß BMC Bioinformatics 2014 15:89 doi:10.1186/1471-2105-15-89 - Contact: tssar@tbi.univie.ac.at