Hello there,
I am trying to looking for homologous genes using the PSI-BLAST function.
1.) I created a blast database of conserved genes that I had downloaded from uniprot
makeblastdb -in mamA.AA.fasta -input_type fasta -dbtype prot -out mamA_db -parse_seqids
2.) I wanted to query my contigs - assembled from a metagenomics dataset and genes were predicted with the prodigal software - against the database that I have created.
psiblast -query contigs.prodigal.faa -db mamA_db -out mamA.psi.blast -num_iterations 3 -out_pssm mamA.checkpoint -num_threads 10 -comp_based_stats 1 -out_ascii_pssm mamA.pssm
However, it came out with these warning: Warning: [psiblast] lcl|Query_46 NODE_1_length_138104_cov_11.046462_46 # 25949 # 26596 # 1 # ID=1_46;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.407: Warning: Frequency ratios for PSSM are all zeros, frequency ratios for BLOSUM62 will be used during traceback in composition based statistics
Am I doing something wrong here? Will appreciate if someone could help.
Thank You.
Typically warnings are just that - warnings. They can usually be ignored if you know what you're doing. Do you still get results out of your command?
What happens if you run the command without outputting the PSSM?