in silico restricion digestion

[antu82]

Hello,

I currently have illumina sequencing data and already done denovo assembly and the stuffs needed for that project.

Now, I am interested in restriction enzyme digestion followed by sequencing. But before running that project I would like to see how it would look like. So, basically I want to cut already sequenced sequences with some restriction enzyme in silico. I don't want to cut just the consensus sequence but all of those sequences and assemble again and see if those cut sequences assemble to form the same consensus sequence an so forth. I may also want to introduce some randomness if possible like missing some true sites.

Is there some program to do this task. or part of it?

Thank you

[maasha]

Biopieces (www.biopieces.org) contain several tools that may come in handy. digest_seq springs to mind for digesting your reads e.g.:

read_fasta -i reads.fna | digest_seq -p GGATCC -c 1 | write_fasta -o digest.fna -x

To introduce some randomness you can divide your reads into two piles. There is no one-step solution for that, but we can do the following:

read_fasta -i reads.fna | random_records -n 10000 | write_fasta -o random.fna -x

Next we need to subtract the random reads from reads.fna. First we generate a list of IDs from the random reads:

read_fasta -i random.fna | write_tab -k SEQ_NAME -o ids.txt -x

Next we grab those reads _not_ matching:

read_fasta -i reads.fna | grab -i -E ids.txt | write_fasta -o pile.fna -x

Then we can mutate the sequences in the random pile using mutate_seq and indel_seq:

read_fasta -i random.fna | mutate_seq -p 5 | indel_seq -P 5 -D 5 | write_fasta -o random_mutated.fna -x

Now you can collect pile.fna and random_mutated.fna into a simulated set:

read_fasta -i pile.fna,random_mutated.fna | write_fasta -o simulated.fna -x

I hope this illustrates how Biopieces may help you.


Cheers,


Martin

[antu82]

Thank Martin,

Looks very useful. I will look at the program and see if it can answer my question.

Thanks again