Hello,
I want to use BLAST locally and query a remote database
how do you pass a parameter for the database?
exemple : blastall -p blastn -d blast.ncbi.nlm.nih.gov -i ref.fasta -o alignments.txt
Thanks.
Look in the BLAST+ documentation at NCBI about using the "-remote" switch to send your query to the NCBI server farm for processing.
If I remember this correctly, all you need do is add "-remote" to the end of your query command line (but make sure you are running BLAST+, not legacy BLAST).
Look in the BLAST+ documentation at NCBI about using the "-remote" switch to send your query to the NCBI server farm for processing.
If I remember this correctly, all you need do is add "-remote" to the end of your query command line (but make sure you are running BLAST+, not legacy BLAST).
Hello,
thank you,
actually had to add "-remote" at the end of the command
and also use the version "blast+" under linux -> "apt-get install ncbi-blast+"
now it works!
example : blastn -db nt -query spo0A.fasta -out align.txt -remote
thank you again.
Not strictly an answer to your question but you should seriously consider using something like HMMER3 in place of BLAST, which can now only be considered a historical method from the 1990s. There is nothing that BLAST does that can't be done better with other methods. You may have non-scientific justifications for using BLAST, such as "its what I was told to do", but if you are a scientist then you should ask yourself if this stands up to scrutiny under peer review.
Dear Professor Gough,
Thank you for your precious comment !
I will also look closely at the HMMER3 tool who use the method of Markov.
You can also do it in Bioedit. You can create a local database and search it or you can send the query to NCBI
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