repository of small ORFs identified by ribosome profiling

This section provides a summary on the acquisition and processing of the data. For more detailed information, feel free to consult the available literature. Use the navigation bar on the left to navigate trough the different steps.


BLASTp9 (Basic Local Alignment Search Tool protein) searches for AA-sequence similarity between the sorfs and the Non-redundant (NR) protein sequences database (NCBI). Sequence similarity with other proteins can provide additional information about the sorf. For intance 5'-UTR located sorfs predicted to have high sequence similarity with a protein isoform can indicate a false positive sORF. Additionailly sequence similarity can identify "PRIDE hits" that possibly originate from an other protein. The parameters used to run BLASTp are adopted from NCBI, all hits with an E-value of 10 are recorded on innerBLASTp BLASTp is also used to find sORFs with sequence similarity between sORFs identified in distinct species. This can provide additional evidence for functional important sORFs and may facilitate functional characterized in more convenient model organisms. As a threshold for BLASTp an E-value of 0.0000000001 is used as opposed to the BLASTp search against the NR-database.