Hello,
Please can anyone indicate a protocol on how to perform a BLAST search to check for sequence homology/identity of a parasite protein if it exist in humans or not.
Please, I really need the guidelines on how to go about it since it is a prerequisite for drug target discovery and rational vaccine design studies.
Thanks,
1. select the BLAST program.
2. Enter a query sequence or upload a file containing sequence.
3. Select the data base to search.
4. Select the algorithm and the parameter of algorithm for the search.
5.Run the BLAST program
Hello
1: Retrieve a query sequence you want to use and make sure it is in fasta format
2: Navigate to the database you want to search against
3: Select the BLAST programthat will use the query sequence to search the database that you selected.
4: Adjust any parameters, as appropriate
Ref:
http://vlab.amrita.edu/?sub=3&brch=274&sim=1428&cnt=2
https://www.ncbi.nlm.nih.gov/books/NBK153387/
Article Performing a BLAST search of the STRSeq BioProject
In addition to Saleh's good respond, i should add that you can often try to exclude and /or include certain species within the database your intend to query, when navigating via the BLAST parameters.
Hello Nkemngo Francis Nongley
For drug target discovery and rational vaccine design studies, it is really important to check the similarity between the parasite and the human protein,to avoid an auto-immunity from getting evoked. So you gotta perform Blast P of your epitopes, with the human proteome in particuar to check for any possible hits, that signify similarity. In case you donot find any hit, then you are good to go with the proteins you are having.
This can be done by performing BLAST P using Reference Sequences database (Ref_Seq).
You can find it in the following link:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins
Click on the above link and do as follows,
- Paste the FASTA sequence of your protein in the space given
- Select Reference proteins option in the database
- Type 'Homo sapiens' in the organism section
- Select BLAST P in the algorithm section
- click on the BLAST button
Hope it helps.
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