Turn Off Blast Search On Reverse Complement Strand In Blastn

To disable the reverse complement strand search in BLASTn, you can use the -strand option, which controls which strand of the query sequence is searched against the database. By default, BLASTn searches both strands (the forward and reverse complement) of the query sequence.

To prevent the reverse complement from being searched, follow the steps below:

Step-by-Step Instructions

1. Using the -strand Option in BLASTn:

   The -strand option controls which strands are used during the search:

   • -strand both (default) searches both strands of the query.
   • -strand plus searches only the forward (top) strand.
   • -strand minus searches only the reverse (bottom) strand.

   To turn off the reverse complement search, use the -strand plus option to search only the forward strand.

2. BLASTn Command Example:

   Suppose you have a query sequence query.fasta and a database nt. To search only on the forward strand, use the following command:

   bash

   Copy code

   blastn -query query.fasta -db nt -strand plus -out results.out


   Here:

   • -query query.fasta: specifies the input query sequence file.
   • -db nt: specifies the BLAST database to search against (e.g., the nucleotide database).
   • -strand plus: ensures that only the forward strand is used for the query sequence.
   • -out results.out: specifies the output file for the results.
3. Using BLAST+ Online Interface:

   If you’re using the NCBI BLAST+ web interface, you can choose the strand option directly from the web form:

   • Under the Algorithm parameters section, look for Strand.
   • Select Plus (query strand only) to disable the reverse complement strand search.
4. Checking for Specific Matches:

   You can also filter the results for strand-specific matches by processing the output based on the strand information in the alignment. This can be done programmatically using Python, Perl, or R, but the basic approach is to ensure the search only considers the forward strand using the -strand option.

Example Script (Python):

If you want to automate the process of running BLASTn with the forward strand option in Python, you can use the subprocess library:

This script runs BLASTn with the specified parameters, ensuring that the search is only done on the forward strand.

Other Considerations:

• Filtering Results: If you’re working with large datasets, you can further filter BLAST results based on strand information post-processing.
• Software/Tools: Apart from NCBI BLAST, there are other BLAST-related tools and interfaces (such as BLAST+ standalone, Galaxy, and BioPython) where you can specify the strand option.

By following these steps, you can easily turn off the search for reverse complement strands in BLASTn, ensuring that only the forward strand is considered in your search.