Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Genome Annotation Pipeline Help Required

    First post as a user here, so please go easy on me for lack of due diligence

    We have a genome assembled from Illumina data. There is a reference genome of a closely related species (same genus). I downloaded the proteins from this reference genome and sought to map them to our genome using local tblastn, as a homology-based annotation (we also have predicted transcripts from MAKER as an ab initio annotation method).

    I have seen this method used in the literature, but all the method descriptions skip an important step - actually physically mapping the best tblastn hits (from whatever criteria) to the genome.

    I assume there is some way to convert the blast xml output to an annotation file (GFF or similar) - one that conserves the info from the blast (especially protein name and function). I tried looking into Biopython and BioPerl but could not lay hands on the proper method of doing this.

    Can someone please point me in the right direction?

  • #2
    Originally posted by marct View Post
    First post as a user here, so please go easy on me for lack of due diligence

    We have a genome assembled from Illumina data. There is a reference genome of a closely related species (same genus). I downloaded the proteins from this reference genome and sought to map them to our genome using local tblastn, as a homology-based annotation (we also have predicted transcripts from MAKER as an ab initio annotation method).

    I have seen this method used in the literature, but all the method descriptions skip an important step - actually physically mapping the best tblastn hits (from whatever criteria) to the genome.

    I assume there is some way to convert the blast xml output to an annotation file (GFF or similar) - one that conserves the info from the blast (especially protein name and function). I tried looking into Biopython and BioPerl but could not lay hands on the proper method of doing this.

    Can someone please point me in the right direction?
    I'm currently doing something similar using gmap.. I have a transcriptmome that I'm mapping to a genome though.. (we assembled the transcriptome and then the genome of a related species was subsequently released) also have ests that I'm mapping to a genome with gmap. Exonerate I believe does a similar job and has a protein matching mode.. Anyway both these programs will output in gff format

    Comment


    • #3
      Thanks for the reply. As of this moment I am running genBlast and exonerate as well as the tblastn. In all of these cases, I am using the protein database of the model species as the query and my genomic sequence as the target (or database). I'll let you know how it goes.

      Comment


      • #4
        How come the functions of MAKER were not sufficient for your analysis?

        Comment


        • #5
          I am joining this project somewhat in the middle of the process.

          From my understanding, the initial Maker run was ab initio only, we do not have ESTs or RNA-seq data to add to the pipeline. So while important, the SNAP/Augustus etc gene calls from Maker should constitute one line of evidence for our annotations, while direct alignment of homologous proteins coupled with splice-site detection (a la exonerate) should constitute another, homology-based line of evidence.

          Stop me if I'm wrong.

          Comment


          • #6
            Hang on..

            I thought MAKER was just for ab initio. You can use that to bring together ESTs and RNA-Seq data too?

            That's what I have. I'm just mapping my transcripts to the ESTs at the moment

            Comment

            Latest Articles

            Collapse

            • 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
            • 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

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 05-14-2024, 07:03 AM
            0 responses
            20 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 05-10-2024, 06:35 AM
            0 responses
            44 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 05-09-2024, 02:46 PM
            0 responses
            56 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 05-07-2024, 06:57 AM
            0 responses
            43 views
            0 likes
            Last Post seqadmin  
            Working...
            X