bbuchfink
Using blast can find results, but diamond has no results
Hi! I need to compare two protein sequences. NCBI's blastp has the comparison results, but Diamond can never find the results. Is it that my parameters are set incorrectly? The two sequences that need to be compared are as follows (the two sequences are only 83 and 42 in length, respectively):
>Putative_mercuric_reductase
MSAIFVPGNAVADKVILKIEGMTUAAUPLIIRKALEGLEGVEKASVSYSKGKGEVVFDPAKVSEKDIVDQVDRIGFRAKVIEE
>JALLOF010000030.1_Nitrospinae_bacterium_AH_259_B05_G02_I21_NODE_30_length_20278_cov_88.0098
MSRREMITTLVLGLLFLGMFVVPAVAELQTVTLTIEGMVUGA
The NCBI blastp result is as follows:
The command I used is as follows:
diamond blastp --db ./diamond/db -q ./query.txt --out ./diamond/result --outfmt 6 stitle qseqid sseqid pident length mismatch gapopen qstart qend sstart send sseq_gapped qseq_gapped evalue bitscore --threads 120 --masking 0 --ultra-sensitive --id 20 -e 1e-2
Thank you very much for your reply!
DIAMOND is not configured to find very short hits by default. I shared some tips how to do this here: https://github.com/bbuchfink/diamond/issues/832
Thank you for your reply!! I try this issue that you mentioned parameters: #607, and it can work.