When we do a nucleotide blast for certain sequences, there are tons of results like "cloning vector" or "synthetic construct". These are plasmids made by researchers. I want to exclude all these from the search, so that only hits from genomes or transcripts show up. I do not want to restrict the search to one or a few specific species, but want to search all species, minus plasmids. Is it possible?
Are you looking at the non-redundant or the REFSEQ databases? Those should have such things removed, especially the REFSEQ.
If your sequence does not have any good hit in the database, you will get random hits. And generally these hits have small query coverage and/or high evalue. You can think what your sequences are before just blasting them.
You can exclude "synthetic construct", "cloning vector", "plasmids" etc. organisms. You can even exclude multiple of them.
Or conversely, you can limit your search to eukaryota, prokaryota and Archea.
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