Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Identifying Single Copy Human Genes

    Hi all,

    I am trying to come up with a conservative list of single copy human genes -- i.e. I want to exclude all genes that may be part of a larger gene family/have highly similar sequence similarity. I've done quite a bit of searching but have not found anything I'm satisfied with.

    My basic approach is to blast the the human transcripts file against itself and filter out transcripts that have significant hits to any other transcripts other than itself.

    My question is, what blast parameters would best accomplish this? I would rather be more conservative.

    Any ideas of suitable cut-offs for the following parameters?

    1. e-value (1e-10)
    2. hit length to query length ratio (50%)
    3. Percent identity (90%)

    Thanks

  • #2
    Do you want as many single copy genes as you can find, or do you want to have high confidence that the genes you find are actually single copy? If a false positive is worse than a false negative then the more stringent your conditions the better.

    Comment


    • #3
      Perhaps looks into OrthoMCL?
      savetherhino.org

      Comment


      • #4
        @ExMachina I would much rather have very few false positives even at the cost of losing true positives. I'm trying to get a reliable subset of single copy genes to calculate some statistics with. Nebelwerfer.

        @rhinoceros I think OrthoMCL would be the perfect solution. Thanks.

        Comment


        • #5
          [QUOTE=jgibbons1;102666]Hi all,

          I am trying to come up with a conservative list of single copy human genes -

          Hi jgibbons1!

          Did you finally manage to have this list? if so do you have any published data that you may be able to share?
          Thanks!!!

          Comment


          • #6
            Are you looking at haplosufficient or haploinsufficient genes?

            Haploinsufficient genes: http://www.nature.com/ejhg/journal/v...g2008111a.html

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Latest Developments in Precision Medicine
              by seqadmin



              Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

              Somatic Genomics
              “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
              Yesterday, 01:16 PM
            • seqadmin
              Recent Advances in Sequencing Analysis Tools
              by seqadmin


              The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
              05-06-2024, 07:48 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, Yesterday, 07:15 AM
            0 responses
            13 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 05-23-2024, 10:28 AM
            0 responses
            17 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 05-23-2024, 07:35 AM
            0 responses
            20 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 05-22-2024, 02:06 PM
            0 responses
            10 views
            0 likes
            Last Post seqadmin  
            Working...
            X