Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Is there a in silico enzyme digestion script?

    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!

  • #2
    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
    To get a BED file:

    Code:
    read_fasta -i genome.fna | digest_seq -p GGATCC -c 1 | rename_keys -k SEQ_NAME,S_ID | write_bed -xo fragments.bed
    Or to do both in one go:

    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

    Comment


    • #3
      You definitely should take a look at the remap tool from the EMBOSS package.

      Cheers,
      Adhemar

      Comment


      • #4
        thank you!

        Thank you for helping me out! I will give a try.

        Comment


        • #5
          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


          • #6
            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  
            
            # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
            AND

            run the command

            Code:
            source ~/.bashrc

            Martin

            Comment


            • #7
              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]}}'
              Is it stupid ? I don t understand why this team have so different results ....

              Here is my results for instance : I have 9975 time one nucleotide between 2 CCGG's

              Any idea ?

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Strategies for Sequencing Challenging Samples
                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...
                03-22-2024, 06:39 AM
              • seqadmin
                Techniques and Challenges in Conservation Genomics
                by seqadmin



                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                Avian Conservation
                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                03-08-2024, 10:41 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, Yesterday, 06:37 PM
              0 responses
              8 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, Yesterday, 06:07 PM
              0 responses
              8 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-22-2024, 10:03 AM
              0 responses
              49 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-21-2024, 07:32 AM
              0 responses
              66 views
              0 likes
              Last Post seqadmin  
              Working...
              X