Hi everybody. I used local blastp at terminal for 1628950 small peptides (in one fasta file) against human proteome database. But I could not find 3 expected pairs (peptide query accession - human protein hit accession) while I could find 952 other pairs. I firstly used "-ungapped -comp_based_stats F" options then I tried to change options as "-num_alignments 500 -comp_based_stats F" to increase number of alignments from default value (250). These did not work. I tried "-outfmt 5 -max_target_seqs 50000 -comp_based_stats F". This also did not work. I will try "-outfmt 5 -max_target_seqs 50000 -ungapped -comp_based_stats F" but it also did not work. When I did blastp only these three peptides against human proteome, I could find expected human proteins but by using big fasta file it did not work. How can I solve this problem? Should I increase num_alignments much more or num_descriptions or both? And what is the difference between them? Thanks in advance.
