I have used the command-line version of tRNAscan-SE by Lowe et al. (1997) on the reference genome sequence of C. elegans to predict tRNAs. The programme outputs a table with tRNA locations, amino acid, anti codon, intro locations, tRNA type (functional or pseudogene) along with a score. The score in my dataset ranges from 20.0 to 107.4. After reading the article Lowe et al (2016) describing this tool, I still do not understand how this score comes about and what it means. I understand that:
- the higher the score, the more likely the tRNA is assigned to the correct isotype (amino acid)
- the lower the score, the more likely the tRNA is a pseudogene
My questions are:
- How is the score calculated?
- What does the score mean?
The authors of the tool state that is is 99% sensitive and detects 1 false tRNA in 15 GB of DNA. Does this mean that I do not need to filter my results? What about the confidence in the type of tRNA and whether it is functional or pseudogenised?
Lowe et al (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nuc. Acids 25 Lowe et al (2016) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nuc Acids Web Server issue: W54–W57.