I am looking for a in silico enzyme digestion program which I can input the enzyme name, cognite sequence, and the genome to be scanned against. the output will the size distribution of the resulting fragment, also a BED format file with fragment coordiate, like chrom, start, end etc. Anyone has such a program and would like to share with me. Thanks a lot!
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Hello,
This can be done with Biopieces (www.biopieces.org) using digest_seq and BamHI as an example:
Code:read_fasta -i genome.fna | digest_seq -p GGATCC -c 1 | plot_lendist -k SEQ_LEN -x
Code:read_fasta -i genome.fna | digest_seq -p GGATCC -c 1 | rename_keys -k SEQ_NAME,S_ID | write_bed -xo fragments.bed
Code:read_fasta -i genome.fna | digest_seq -p GGATCC -c 1 | plot_lendist -k SEQ_LEN -t post -o dist_plot.ps | rename_keys -k SEQ_NAME,S_ID | write_bed -xo fragments.bed
Restriction enzyme patterns and cut positions are found at REBASE http://rebase.neb.com - or by typing "rescan_seq --help"
Cheers,
Martin
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You definitely should take a look at the remap tool from the EMBOSS package.
Cheers,
Adhemar
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I have difficulty to run the command. I installed the packages in my desktop, and follow the instructions which listed in the web. I am not sure whether the code is sourced, and I run the test code, it seems nothing changed. Could you give more detailed information on how to install it and test it since I am a bench scientist, not that familiar with the command line program. Thanks
nexgen@nexgen-desktop:~/Desktop/biopieces$ bp_test
bp_test: command not found
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Did you add the following section to your ~/.bashrc file:
Code:# >>>>>>>>>>>>>>>>>>>>>>> Enabling Biopieces if installed <<<<<<<<<<<<<<<<<<<<<<< # Modify the below paths according to your settings. # If you have followed the installation step-by-step as described above, # the below should work just fine. export BP_DIR="$HOME/biopieces" # Directory where biopieces are installed export BP_DATA="$HOME/BP_DATA" # Contains genomic data etc. export BP_TMP="$HOME/tmp" # Required temporary directory. export BP_LOG="$HOME/BP_LOG" # Required log directory. if [ -f "$BP_DIR/bp_conf/bashrc" ]; then source "$BP_DIR/bp_conf/bashrc" fi # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
run the command
Code:source ~/.bashrc
Martin
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Hi, I am confronting the same problem, in silico digestion for CCGG .
I have a file with hg19 and one line per chromosome sequence and I do :
Code:cat hg19.txt | sed "s/[COLOR="DarkRed"]CCGG[/COLOR]/\n/g" | awk '{l=length($1); mem[l]++;} END{for(i=0;i<=1000;i++){print mem[i]}}'
Here is my results for instance : I have 9975 time one nucleotide between 2 CCGG's
Any idea ?
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