I set up the NCBI BLAST standalone on my computer and downloaded nt.[01-39].tar.gz as my subject database. When a query an example sequences with the standalone BLAST I receive less hits than online or when I use biopython qBlast (result_handle = NCBIWWW.qblast("blastn", "nt", record.seq, expect=10, hitlist_size=100000))
When I use qBlast or the online tool I have 2564 hits compared to 506 hits when I use the standalone BLAST (blastn –query mysequence.txt –db nt –out mysequence_vs_NT.txt -outfmt 17)
Interestingly I get 1623 hits if I use the parts of the database one by one. So it doesn't match with the online hits but is "better" than the standalone result. (blastn –query mysequence.txt –db nt.[0-39] –out mysequence_vs_NT[0-39].txt -outfmt 17)
How can I get all hits with the standalone BLAST? I appreciate all your help and input!