Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • any in silico enzyme digestion program for genome

    Does someone know any program for in silico enzyme digestion. I am a web lab scientist , need to do a computational simulation for whole genome enzyme digestion. I need a program which has the input option for genome, enzyme, the resulting fragment size range, also whether the fragment is unique. The output file are something like the Bed file like format with chr, start, end, and fragment size etc. It will be great that it can also give a distribution plot for the fragment. Thanks a lot!!!! I will be really appreciate.

  • #2
    This paper has a program for it but I don't know if it is available:
    Zhou et al. J of Bacteriology 2004

    Comment


    • #3
      There is an instrument!

      Hi -
      The reference cited is the basis of an instrument that does this type of mapping made by OpGen. See OpGen.com

      Comment


      • #4
        Hi sunsnow86,

        Did you manage to find thein-silico digestion software you were looking for? I'm looking for the same now.

        Comment


        • #5
          Counting RE site in bigger genome

          Dear sunsnow86 and fastidiousme,
          Did you find somw tool/scripts to estimate restriction enzyme sites in bigger genomes? I am also looking for the same.
          Regards,
          S

          Comment


          • #6
            Probably multiple tools out there, but it is also a good project for a beginning bioinformatics student. Without excessive bells-and-whistles, should be about a page of code in any high-level language with good bioinformatics library support (e.g. Perl, Python, Java)

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Essential Discoveries and Tools in Epitranscriptomics
              by seqadmin


              The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
              Yesterday, 07:01 AM
            • seqadmin
              Current Approaches to Protein Sequencing
              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...
              04-04-2024, 04:25 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 04-11-2024, 12:08 PM
            0 responses
            39 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 10:19 PM
            0 responses
            41 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 09:21 AM
            0 responses
            35 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-04-2024, 09:00 AM
            0 responses
            55 views
            0 likes
            Last Post seqadmin  
            Working...
            X