Hello everyone,
I created a standalone blast database of a few Y-STR marker sequences and their respective allele variants. I used the following command to make the database :
- C:\Users\BLAST+\bin>makeblastdb -in "C:\path\to\combined database\sequence" -dbtype nucl -out "C:\path\to\output\folder"
I also created a multifasta file (5 sequences with sequence IDs - sequence1, sequence2,etc.,) from the very sequences I used to make the database. I used the following command to run my query:
- C:\Users\BLAST+\bin>blastn -query "C:\path\to\input\query sequence" -db "C:\path\to\database" -out "C:\path\to\results folder\results.txt" -outfmt 6
This is where I faced the issue of only getting results for 2 of the 5 input sequences, three of the sequences showed 0 hits. The issue persisted when I ran the same query file in NCBI's official BLAST page. I also created a separate database of just the undetected sequences and still the query sequences were not being detected.
Has anyone faced a similar issue? Any insights would be greatly appreciated
Hello!
Is your query fasta correctly formated? :) If your query sequences are exactly the same or similar with those from database, you should get a result or more results for each query. You should also verify with a for loop and align each sequence at a time (kind of: for i in *.fasta; do blastn -query $i -db "C:\path\to\database" -out $i"C:\path\to\results folder\results.txt" -outfmt 6). :)
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