Hello, i have a fasta file with 7600 nucleotide sequences, i have a local nr database formated for blast, with makeblastdb, i don't use formatdb because it give errors (zero length sequences).
I blast all my 7600 sequences, but only 20! have a hit against the nr database.
This looks very strange to me, so i pick some sequences, and blast manually from the NCBI website, and obviously this give to me results for every sequence..
so, 2 questions, what could be wrong in my local blast?
and two, i can blast all my sequences using the NCBI webpage, but i can't figure out how to download all the results at once, instead i have to download manually one by one, and i can't do this for 7600 sequences, any workaround?
thanks in advance