User Manual
Welcome to Tripal Sequence Similarity Search (formerly known as Tripal Diamond)
The main page for submitting a Diamond or BLAST job will look similar to this:
Your first step is to choose which type of query you will be running. This will expand further options. Your choices are
- Protein
- Genomic (coding or non-coding)
Once you have selected a query type, you will be presented with what type search you will perform. This will depend on whether the database you are going to search against is a Protein database or a Nucleotide database.
The following programs are available:
BLASTX -> Nucleotide query vs Protein database -> Diamond
BLASTP -> Protein query vs Protein database -> Diamond
BLASTN -> Nucleotide query vs Nucleotide database -> BLAST
TBLASTN -> Protein query vs Nucleotide database -> BLAST
Your options will be presented in a drop down.
Depending on your choices from the first two steps, you will be presented at least 1 list of possible target databases to search against. These are provided by the website. You can choose exactly 1 from any of these lists.
Alternatively, you can choose to upload or paste your own database. By clicking "Upload your own Database/Target", forms will appear for you to fill out.
If you choose to upload a file, make sure to hit 'Upload' before proceeding.
The next step requires you to either paste your query sequence into a textbox or upload your file. Remember: when uploading a file, make sure to hit 'Upload' before proceeding.
You may need to tweak some settings for your search. If you click on 'Advanced Options', an area will expand and let you alter some parameters for your search.
The options presented are
- E-Value
- Target Coverage
- Query Coverage
- Max Alignments
Once you are satisfied with the options and data you have uploaded, click ”Submit". Your job will automatically be queued into the system. You will be given a link to check on the status and results of your job. Additionally, you will also be notified via email when your search is complete.