wrpearson
commented
8 months ago Yes, ssearch36 will only return 45k alignment scores. It looks at all the sequences, and returns the 45K best. There is a parameter in defs.h that sets the 45K. You can make it any number you want.
Bill Pearson
On Jan 20, 2024, at 3:49 AM, brush111111111111 @.***> wrote:
What I originally wanted to do was get all pairwise sequence identity of 2 relatively large sets of sequences (~100k seqs). What I found was that when I give ssearch36 a query file with 1 sequence, and a library file with 100k sequences, ssearch only returns (randomly?) the alignment seuqence identity for 45000 sequences from the library file? The exact command I use is as follows:
ssearch36 -s BL62 -E 1e+10 -C 10 -T 4 query_1_seq.fa library_100k_seq.fa
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brush111111111111
What I originally wanted to do was get all pairwise sequence identity of 2 relatively large sets of sequences (~100k seqs). What I found was that when I give ssearch36 a query file with 1 sequence, and a library file with 100k sequences, ssearch only returns (randomly?) the alignment seuqence identity for 45000 sequences from the library file? The exact command I use is as follows:
ssearch36 -s BL62 -E 1e+10 -C 10 -T 4 query_1_seq.fa library_100k_seq.faThe solution I have now is simply to just chunk the sequence library file into sets of ~40k seqeunces.