Accessing the BLAST Service on the PATRIC Website¶
The BLAST Service can be accessed from the SERVICES tab on the PATRIC homepage. The BLAST Search allows you to search against public or private genomes in PATRIC or other reference databases using a DNA or protein sequence and find matching genomes, genes, RNAs, or proteins.
Clicking on BLAST from the SERVICES tab will open up the BLAST landing page where researchers can do nucleotide or amino acid BLAST searches.
- Loading a sequence. Cut and paste a sequence into the Sequence box.
- Choosing a type of BLAST. Depending upon the sequence, this will
open the drop down box under Program, showing the types of BLAST
available. Definitions of the types of BLAST searches are as
- BLAST: searches nucleotide databases using a nucleotide query
- BLASTP: searches protein databases using a protein query
- BLASTX: searches protein databases using a translated nucleotide query
- TBLASTX: searches translated nucleotide databases using a translated nucleotide query
- TBLASTN: searches translated nucleotide subjects using a protein query
- Selecting a database. PATRIC provides a variety of databases that selected sequences can be compared to.
- BLASTing against gene features or contigs. Depending upon query type, researchers will be able to choose to search entire genomes or limit the search to only features. When BLASTN, TBLASTN, or TBLASTX are selected, researchers can choose to search against either contigs or features. When BLASTP or BLASTX are selected, the search is limited to features.
- Adjusting the BLAST parameters. You may use the Advanced Options to adjust both the number of hits returned, and the E value threshold.
- Submitting the BLAST job. Once the sequence has been uploaded, the program and database selected, the BLAST parameters adjusted, the job can be started by clicking the Search button at the bottom of the page.
- Submitting another BLAST job. At the top of the BLAST result page, researchers can click on the Edit from and resubmit button to initiate another BLAST job.