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This page provides a description of the output page of the Secmarker web server.

The top section of the output page contains the links to the output files. The files are stored for a limited period of time (one week), and after that all traces of your search will be deleted. These output files are meant to be downloaded if you want to save in your computer the results of your search. Output files includes popular formats such as GFF and fasta which can be used for further processing with other programs. Below the links section, each result is shown.

tRNA-Sec prediction

Each results contains an image of the cloverleaf secondary structure of the candidate tRNA-Sec. The base pairs are colored according to the arm of the tRNA (acceptor arm, D arm, anticodon arm, variable arm and T arm are colored in red, yellow, green, blue and purple, respectively). Wobble pairs (G-U, U-G) are indicated with a less saturated color. The UCA anticodon (in the anticodon arm) is indicated with circled residues. If the tRNA-Sec prediction is complete (A-stem with 9 bp, or 8 bp in the case of bacteria), the discriminator base is included in the output, and circled in tRNA image.

Finally, each prediction contains the tRNA sequence and secondary structure: