Finding homology stretches in FASTA files

Question

[blasco]

I would like to find short stretches of sequence (i.e. 18-20 nt) present in two fasta files. The idea is to identify those matches in sequences of otherwise distant organisms, or distant metagenomes. I have seen programs that look for similar reads, but those would not identify short stretches within the reads. Is there any program that can do that?.

[GenoMax]

Sounds like you are looking to identify prevalent k-mers (18-20) in your sequences. kmercountexact.sh from BBMap may be worth looking at.

$ kmercountexact.sh in=file.fasta out=counts.txt fastadump=f k=20 overwrite=t