About TromER

The TROMER Web service of the Swiss Institute of Bioinformatics (SIB) consists of gene prediction entries, or transcriptome units, of the following genomes: human, mouse, rat, drosophila and worm. Gene predictions are based on data from RefSeq and EMBL/GenBank. This is a moderately conservative set of predictions, requiring the support of either one GenBank full length RNA sequence, one RefSeq RNA, or one spliced EST.
The TROMER-predicted track includes both protein-coding and non-coding transcripts. The CDS are predicted using ESTScan.

The web service provides a quick-search mechanism based on TROMER accession identifiers (e.g. HTR005756 for the tumor necrosis factor alpha TNF), NCBI gene identifiers (e.g. 7124), SwissProt identifiers (e.g. P01375), and gene names or HUGO symbols (e.g. TNF).
We are planning to improve the search scheme to possibly include more detailed and reliable genome annotation.
Each transcriptome unit can be linked to the most popular life sciences databases such as the NCBI Entrez cross-database portal, SwissProt, CCDS at NCBI and GenBank.

The Web interface also provides visualization of TROMER-generated splicing graphs in two forms:

Together with the TROMER splicing graphs, direct HTML links to UCSC and Ensembl are provided in order to visualize the transcriptome unit within its genomic context.

SIB Genes tracks as well as splicing graphs have been integrated in the UCSC Genome Browser.

Last update 13 May 2010