The library of sequences that we provide here consists of 24 databases generated from transcriptomic data acquired from Uca minax (commonly known as the red-fiddler crab). The crustacean family is one that is sparsely represented in current genomic databases. Thus, these databases provide a unique opportunity to explore this group of organisms and sample the gaps in existing genomic data.
Our searching mechanism leverages BLAST to perform querying on these custom-built databases. Basic Local Alignment Search Tool (BLAST), finds regions of local similarity. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences and identify library sequences that resemble the query sequence above a certain threshold.
1. Determine the sequence you would like to search for. It can be any length and should be in FASTA format.
2. To upload your sequence you can either copy and paste it into the textbox or directly upload your file using the browse button. Each option has a radio button beside it. To enable the method of uploading that you would like to use you must make sure that the corresponding button is selected.
3. Select one or more of the databases by clicking the checkbox to the left of the title. To see a more detailed description of each database, hover over the check box next to the title and a text box will appear with additional information.
4. Give your run a meaningful title.
5. Submit your search. Depending on the number of databases that you choose and the length of your search sequence, the alignment may take up to a few minutes to complete. The result will appear as soon as it is ready. If you queried multiple databases your results for each one will be shown in seperate windows underneath the main search area.