Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • alternate assembly

    Hi all,
    I wanted to ask what is alternate assembly in blast and how I should treat it. I mean that I find structural differences when I am doing a mapping project, but then, when I check it in blast, I find that it firs perfectly alternate assembly, so it is not a real variation? how can I avoid this situation?
    THANKS!!!

  • #2
    The alternate assembly or often assemblies are just that alternate build of your given genome from different individuals. The simple solution is to first pick the reference genome you want to use then in blast settings select to blast just this reference so you don't get hits from all the possible assemblies. Unfortunately, Watson and Venter are not identical twins so even their builds are not identical...go figure

    Comment


    • #3
      alternate assembly

      Thank you. Yes, I understand that there might be assemblies from different people and I can set the settings in blast not to see it, but the question is not whether I see it or not but whether the structural difference I found when mapping to the reference genome is a mutation, and if I understand correctly, if there is an alternate assembly like this, this is not a real mutation?

      Comment


      • #4
        Originally posted by litali View Post
        Hi all,
        I wanted to ask what is alternate assembly in blast and how I should treat it. I mean that I find structural differences when I am doing a mapping project, but then, when I check it in blast, I find that it firs perfectly alternate assembly, so it is not a real variation? how can I avoid this situation?
        THANKS!!!
        True versus false variation is dependent on your research question. If you are looking for novel disease causing structural variations you can use blast as you are doing to filter out things in the other assemblies or use some of the various databases to exclude known variants in other datasets. But if you are looking of misrepresented variants you are talking more about annotation and counting versus filtering. But the short answer is if the variant is in another assembly it is not a real/novel variant. So you should filter your reference genome variant list against a list of known variants which are available in a number of databases

        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...
          04-22-2024, 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
        59 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        57 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        51 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-04-2024, 09:00 AM
        0 responses
        56 views
        0 likes
        Last Post seqadmin  
        Working...
        X