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!
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
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
-
You definitely should take a look at the remap tool from the EMBOSS package.
Cheers,
Adhemar
Comment
-
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
Comment
-
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
Comment
-
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 ?
Comment
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
31 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
33 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
28 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment