Andreas Tille <ti...@debian.org> writes: > ncbi-blast+-legacy (>= 2.5.0-2~) | blast2
Yes, this is an appropriate dependency for anything that historically listed blast2 and continues to use legacy command names such as bl2seq. > Could you give some hint for a patch to fix this test suite error: Good question. The error from the underlying blastn command (buried in the middle of the log) is BLAST engine error: Error: Gap existence and extension values 0 and 0 are not supported for substitution scores 1 and -1 3 and 2 are supported existence and extension values 2 and 2 are supported existence and extension values 1 and 2 are supported existence and extension values 0 and 2 are supported existence and extension values 4 and 1 are supported existence and extension values 3 and 1 are supported existence and extension values 2 and 1 are supported existence and extension values 4 and 2 are supported existence and extension values Any values more stringent than 4 and 2 are supported I've tried fiddling with parameters to address this error, but so far haven't been able to get blastn to report *any* hits for these test cases, perhaps because the sequences are too short. I'm also concerned that pynast.util.blast_align_unaligned_seqs invokes bl2seq with the -VT flag, which historically requested the old BLAST engine. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
