Makblastdb And Low Complexity Regions

Question

[Raygozak]

Hi i want to create a blast database from sequences that under blast are marked as "low complexity", is there a way to make makeblastdb turn off this filtering?

i'm aware that the sequences might be "low complexity" but under my specific application the sequences happen to be that way.

EDIT: the error i'm getting is at the time of building the database:

Ignoring sequence 'lcl|11859' as it has no sequence data Ignoring sequence 'lcl|11860' as it has no sequence data Ignoring sequence 'lcl|11861' as it has no sequence data Ignoring sequence 'lcl|11862' as it has no sequence data Ignoring sequence 'lcl|11863' as it has no sequence data Ignoring sequence 'lcl|11865' as it has no sequence data Ignoring sequence 'lcl|11866' as it has no sequence data Ignoring sequence 'lcl|11869' as it has no sequence data ... ... ..

[Neilfws]

The error is more of a warning and it means what it says. If you go back and examine the fasta file, you'll probably find that those sequence IDs have a header but no sequence line.

Answer 1

[VS]

Just set the option -F=F while running blast to turn the low complexity filter off.

EDITED to add :

makeblastdb does not mask low complexity regions by default. So your error is likely not due to LCRs but something else. You should look at the sequences whose ids are giving you the error. What is their length?