How to search by tRNA sequence
This function uses BLAST to search for tRNA genes similar to the query sequence. Clicking on the "Search by Sequence" menu item will bring up the input form. There are two required items for initiating the search:
- database - the tRNA genes the query sequence will be searched against
- query sequence - the sequence can be entered in the text field or submitted by uploading a FASTA file
Optionally, users can select the E-value threshold (Expect) and word size other than default values or add advanced options. To understand more about BLAST options, please check out the documentation from NCBI.
The BLAST results are divided into two sections: 1. List of result hits ordered by E-value 2. Pairwise alignment of each result hit
The smaller the E-value, the higher similarity is found between the query sequence and target sequence. Clicking on the "L" link at the end of each entry will jump to the corresponding pairwise alignment (illustrated by the numbering indexes on the left of the first three result hits in the figure above).
The BLAST hit at each pairwise alignment includes the following information of the target tRNA gene: * species name (for example, Homo sapiens) * genome assembly abbreviation (for example, Hsapi38 stands for Homo sapiens GRCh38) * GtRNAdb gene symbol (for example, tRNA-Gly-GCC-2-6) * tRNAscan-SE ID * isotype * anticodon * gene length * tRNAscan-SE bit score * genomic coordinates of the locus
If the BLAST hit sequence name is enabled as a link, clicking on it to launch the UCSC Genome Browser showing corresponding gene locus.