Hi Andreas,

That seems to correspond to tRNA genes (like E.coli trna gene nomenclature), so I think you can find anticodon info just looking on these genes in ncbi or other db.

...but this is just a guess :)

Cheers,

Stepan

Thanks for your answer Stepan. However, I already know the anticodon of each of my annotated tRNAs, the issue is to assign the name using the E. coli tRNA genes nomenclature. I saw some E.coli annotated genomes and there are distinct tRNA genes (for example asnQ and asnW) that codify for Asn-tRNAs with the same anticodon. So, it seems that anticodon is not the criteria for gene name assignment.

Although I can't give specific advice (not having used tRNAcc, adn, I have two general comments.

First, there is no "rule" for annotation of tRNA genes -- in E. coli, for example, many tRNA genes were first identified as genetic loci in the biosynthetic pathway for a particular amino acid. The one-letter identifier is completely arbitrary: it might be the order in which mutants were isolated, or a guess at the function of the gene product. For example, tyrA is an enzyme of tyrosine biosynthesis, tyrP is a tyrosine transPorter, tyrS is tyrosyl-tRNA-Tyr Synthetase, and tyrT, tyrU, and tyrV are three different loci encoding tRNA-Tyr, (tyrT is the one which can mutate to become the classical suIII amber suppressor tRNA.)

Second, the paper describing tRNAcc indicates that the program uses the name of the tRNA _gene_ as annotated in the genome being examined. Are the names of your tRNAs (e.g., asn-GTT) the same as the names of the corresponding genes present in the genomic sequence file you are searching? For exaple, if tRNAcc does not recognize or accept "asn-GTT" as a valid gene name, you could manually rename it to look like standard bacterial nomenclature -- say "asnG". However, I think it's more likely that, although your tRNAs are named "asn-GTT", etc., the genetic locus encoding this tRNA has a different name.

Finally I found that you can use any name for tRNA genes. The only requirement is that the same name must be used in both the coordinates file and in the "tRNA genes being analyzed" section. I'm currently using the web-based platform available in Mobilome Finder website, and got the expected results. However, I had many problems with the files used for the analysis (for example with Identify Island algorithm). As stated in the website, the format required for those files is simply categories of values separated by tabs. I generated such files exporting from excel, but they never were recognized by the program. The only way I found where the algorithm worked was to rewrite the files provided in the examples described in the same website. I was wondering if someone else have experimented such complications.