Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Glimmer vs Prokka

    Hello,

    I am wondering if there is some cross-over in the functions of Glimmer and Prokka. As I understand it, Glimmer is able to predict orf's and extract them. Prokka is is used for annotation. Does Prokka therefore also do orf/gene prediction also?

    I've tried to see this for myself but am struggling to properly install Prokka. Glimmer seems to behave exactly as I'd expect.

    Thanks!

  • #2
    Yes, you are right.
    Glimmer is just for gene prediction, while prokka is a kind of all-in-one tools, doing both, gene prediction (or, to be more accurate "feature prediction" as not only genes but also rRNA and tRNA prediction can be included) and annotation.

    Comment


    • #3
      prokka uses Prodigal (http://prodigal.ornl.gov/) for its ORF predictions.

      Comment


      • #4
        Thank you for the help. It was all the encouragement I needed to carry on and get PROKKA working and ditch Glimmer!

        Comment


        • #5
          Good luck with Prokka installation. Though it is a handy tool, it has a scary list of requirements and I couldn't get over it in three attempts so far and gave up for now.

          Comment


          • #6
            I ended up giving up installing it on my Linux laptop and did a clean install of Linux on a partition of my Windows computer.

            Then installed on there and it worked... Didn't really SOLVE my problems but I can use it so I'll take that for now since it's the first step in my work.

            Comment

            Latest Articles

            Collapse

            • 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
            • 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

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 04-11-2024, 12:08 PM
            0 responses
            18 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 10:19 PM
            0 responses
            22 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 09:21 AM
            0 responses
            17 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-04-2024, 09:00 AM
            0 responses
            49 views
            0 likes
            Last Post seqadmin  
            Working...
            X