Help page
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
- tRNA-Sec id: Every tRNA is assigned a numeric incremental id.
- Model: which model (eukarya, bacteria or archaea) the predicted tRNA-Sec fits best.
- Chromosome: the fasta header of the sequence where the prediction resides. If no fasta header was present in input, it will be reported as "your_sequence".
- Strand: the strand on which this tRNA was found: + means it was found on the sequence as it was input, - means it was found on its reverse complement.
- Positions: these are the positions of the tRNA along this target sequence. The first position is indicated by 1.
- Infernal score: bit score obtained by cmsearch, it indicates how well the sequence fits the model.
- Discriminator base: in tRNAs, the base preceding the CCA sequence at the 3' end of the mature tRNA is important for aminoacylation. The CCA sequence is not encoded in the genome, and it is not included in the output sequence. Commonly, tRNA-Sec present a guanine discriminator base.
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:
- RF: the correspondence between the model and the candidate tRNA. The capital letters correspond to each of the tRNA arms (A, anticodon arm; D, dihydrouridine arm; C, anticodon arm; V, variable; TψC arm), and are highlighted using the same coloring scheme as the image. "acd" indicates the position of the anticodon triplet. "=" corresponds to single stranded nucleotides in apical loops, "." or "," correspond to single stranded nucleotides.
- SEQ: the nucleotide sequence of the tRNA, in RNA letters.
- SS: the secondary structure for the tRNA. This is predicted by cmsearch, and may differ from the minimum free energy structure of this sequence.
