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GtRNAdb:tRNA data example analysis, I believe that many inexperienced people do not know what to do, so this paper summarizes the causes of the problem and solutions, through this article I hope you can solve this problem.

GtRNAdb contains tRNA sequence information of different species. These tRNA are predicted by tRNAscan-SE 2.0 software. The official website is as follows.

Http://gtrnadb.ucsc.edu/

The latest version contains tRNA sequences of more than 4300 species. The detailed statistics are as follows.

Through this website, we can retrieve the corresponding tRNA results of species, and we can also make BLAST comparisons.

1. Retrieval function

Support to search through species and screen the interested species according to the evolutionary relationship. The link is as follows

Http://gtrnadb.ucsc.edu/browse.html

Click on the triangle symbol to expand, and then filter the corresponding secondary classification. Take hg38 as an example, the search results are linked as follows

Http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi38/

Through the menu bar on the left, you can view the corresponding information in detail. From the FASTA Seqs menu, you can download the tRNA sequence.

2. Blast alignment function

Determine the input sequence type by comparing the tRNA database. The link is as follows

Http://gtrnadb.ucsc.edu/blast.html

It should be noted that in some species, there are repetitive sequences derived from tRNA, and the primary structure of these sequences is very close to tRNA, so there will be some false positive results in the predicted results of tRNAscan-SE. GtRNAdb uses a specific algorithm to filter the results of direct prediction of tRNAscan-SE to reduce the false positive rate.

For the known species in the database, it is recommended to directly use the sequence in the database, and then directly use tRNAscan-SE to predict the species that are not in the database.

After reading the above, have you mastered the method of example analysis of GtRNAdb:tRNA data? If you want to learn more skills or want to know more about it, you are welcome to follow the industry information channel, thank you for reading!

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