Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • create the missing GFF

    Hi,

    This could be a trivial question. I have a de novo assembled genome and predcited proteins in fasta format. However, the accompanying GFF files are missing. What's the best way of creating the GFF file? Is it: blast proteins vs genome and then something like blast2gff using the blast result?

    Thanks.

  • #2
    You have not said anything about the size of the genome you are working with but you could perhaps use MAKER (http://gmod.org/wiki/MAKER) which will make GFF3 files.

    Otherwise you can build the file yourself by parsing the information you have to fit the GFF3 format: http://www.sequenceontology.org/gff3.shtml

    Comment


    • #3
      Originally posted by GenoMax View Post
      You have not said anything about the size of the genome you are working with but you could perhaps use MAKER (http://gmod.org/wiki/MAKER) which will make GFF3 files.

      Otherwise you can build the file yourself by parsing the information you have to fit the GFF3 format: http://www.sequenceontology.org/gff3.shtml
      Thanks for your reply GenoMax. Assembly size is ~400mb with ~250000 scaffolds(estimated Genome size ~480mb). Maker was was used to find the genes. Output of maker was the predicted transcripts, prtoteins and their corresponding gff file. However, unfortunately we only have the predicted proteins now nad lost other files. Hence instead of running the time consuming Maker pipeline again, I was wondering is their a way of mapping/aligning the proteins aganist the genome just to create the gff file?

      Comment


      • #4
        Originally posted by fahmida View Post
        Thanks for your reply GenoMax. Assembly size is ~400mb with ~250000 scaffolds(estimated Genome size ~480mb). Maker was was used to find the genes. Output of maker was the predicted transcripts, prtoteins and their corresponding gff file. However, unfortunately we only have the predicted proteins now nad lost other files. Hence instead of running the time consuming Maker pipeline again, I was wondering is their a way of mapping/aligning the proteins aganist the genome just to create the gff file?
        Out of curiosity how long was the original Maker run? Day(s)/week? It is a pity that you lost the predicted transcripts file otherwise this would have been easier.

        It may be more work than necessary to re-map the proteins back to the scaffolds and then parse the results to make the GFF file.
        Last edited by GenoMax; 09-11-2013, 05:05 PM.

        Comment


        • #5
          Originally posted by GenoMax View Post
          Out of curiosity how long was the original Maker run? Day(s)/week? It is a pity that you lost the predicted transcripts file otherwise this would have been easier.

          It may be more work than necessary to re-map the proteins back to the scaffolds and then parse the results to make the GFF file.
          Maker run took more than 2 weeks :-(

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Exploring the Dynamics of the Tumor Microenvironment
            by seqadmin




            The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
            07-08-2024, 03:19 PM
          • seqadmin
            Exploring Human Diversity Through Large-Scale Omics
            by seqadmin


            In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
            06-25-2024, 06:43 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Today, 11:09 AM
          0 responses
          15 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-19-2024, 07:20 AM
          0 responses
          147 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-16-2024, 05:49 AM
          0 responses
          121 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-15-2024, 06:53 AM
          0 responses
          111 views
          0 likes
          Last Post seqadmin  
          Working...
          X