Thank you for your prompt response!
I am using Blast for Linux 64 bit downloaded from:
The command line I am using is: blastall -p blastn -F F -W 16 -i <inputfile.fa> -d <knownsequences.fa> -o <outputfile.fa>
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It should "just work".
Which flavour and version of standalone BLAST do you have (the NCBI "legacy" version in C, the new NCBI BLAST+ written in C++, or one of the 3rd party BLAST implementations)?
What BLAST command line are you using?
Have you checked your FASTA files are using the right new line characters for your OS? The command unix2dos or dos2unix can help here. Also try this to count the entries:
grep -c "^>" your_file.fastaLeave a comment:
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BLAST Help
Hello all,
I am trying to compare two .fasta files with many fasta sequences within both the files using Blast. But for some reason Blast is considering only first sequence from the fasta files. I am not sure what parameter I should use (for standalone BLAST) to compare all the sequences of both the files.
Please let me know if anyone knows how to do it.
Thank you!
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