BLAST
can be run using any of several interfaces, including:
ncbi-blast
program suite in a terminalBLAST
serverBLAST
?BLAST
search are offered, which may be appropriate for a particular task.ncbi-blast
at the terminal gives you full control over how to use the program, and allows you to readily build custom databases (useful for proprietary information). However, you are limited to the computing power you have available. Happily, BLAST
doesn't require excessive amounts of computing resources and for many tasks a desktop or laptop machine is sufficient.BLAST
- either locally or using the web interface to the NCBI servers - allows for repeated searches, and automated integration of the search results with arbitrary data-processing tasks and other analyses.BLAST
webpage. Scrolling up-and-down the page indicates several available BLAST
tools, including:
BLASTN
- query a nucleotide sequence against a database of nucleotide sequences)BLASTP
- query a protein sequence against a database of protein sequences)BLASTX
(query a nucleotide sequence against a database of protein sequences)TBLASTN
(query a protein sequence against a database of nucleotide sequences)BLASTN
interface.Sequences can be typed or copied and pasted into the "Enter Query Sequence" box, but they can also be uploaded from an existing FASTA file on your computer. We will do this.
k_sp_CB01950_penicillin.fasta
. Then click on "Open".The file will show up as being selected next to the "Choose file" button.
An interstitial page will appear, reporting the job ID, and giving you runtime information. The page will be updated automatically, and frequently.
Once the job is complete, the results will be displayed as an interactive webpage.
Download
link at the top of the results page.Text
and save the results to output/kitasatospora/ncbi_blastn_query_01.txt
Table(CSV)
and save the results to output/kitasatospora/ncbi_blastn_query_01.csv
BLAST
WebsiteUsing the NCBI BLAST
website: