Hello, all! I want to delete 16s sequence from bacteria genome in either gbk or fasta format. I dob't have any access to commercial software. Are there any open source programs or command line tools that can achieve this? Thanks!
Best, Ben
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benzhang •
1 answer
Using the (free) BBMap package:
If you know the 16S sequences (or those of a close relative), you can align them to the genome to produce a sam file. For example:
mapPacBio.sh ref=genome.fasta in=16S.fasta out=mapped.sam ambig=all maxindel=20
Then you can run BBMask:
bbmask.sh in=genome.fasta out=masked.fasta sam=mapped.sam masklowentropy=false maskrepeats=false
This will mask the sequences covered by the mapped 16S sequences. You can alternatively do it using BBDuk's kmer-based masking mode:
bbduk.sh in=genome.fasta out=masked.fasta ref=16S.fasta k=200 hdist=1 kmask=N
...but I'd suggest the alignment method unless you encounter problems with it.
I'm trying to map bacterial genomes to human microbiome data without considering 16s sequence. Would removing and masking achieve the same result? Thanks!
I see, thank you so much!
Thanks, Brian! Would it work if I find the 16s sequence from the gbk file, and align them to the fasta file, and then mask the aligned region?
Yes, that would work. But I'm not familiar with gbk format. The sequence would need to be transformed to fasta first, which is fairly straightforward.
Got it, Thanks, Brian!
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You could open your fasta file and locate the 16S sequence start (by find) and then delete the range you need with any text editor on *nix/OS X. If you are working on windows then try ApE or SnapGene Viewer.