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  • Best tool for gene prediction ?

    Hi,

    I'm looking for a tool which can predict gene. I have shotgun sequences from 100 to 600bp and this is metagenomic sequences,

    I hesitate between:
    - FragGeneScan
    - Metagene
    - GenMark

    What is the best ? or what tool can you advice to me if it isn't in this list ?

    Thanks

  • #2
    I am looking for this too, any advice?

    Comment


    • #3
      Prodigal
      contains the option for predicting ORF in contigs from metagenomic data
      in all the cases you will have to assemble (or try to) the reads

      do you know if in the list you suggested there is any that can predict without the assembly
      I do not believe that though...

      thank you

      Salvatore

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      • #4
        AS Salvatore suggested, I think this is a good idea to do the metagenomic assembly first with e.g. Ray Meta, Meta velvet, Meta IDBA (and many more...) and later go for gene prediction. There are even tools like MOCAT (http://www.plosone.org/article/info%...l.pone.0047656 ) that can do both.

        Comment


        • #5
          Hello group
          i have predicted set of genes for large eukaryotic genome from ab initio (GlimmerHMM) and evidence (Exonerate) based approaches, now i want to make consensus gene sets from both the predictions. i am facing issues with GLEAN installation, as its installation manual doesn't provide detail on, how to create database of gff files. I have tried Evigan and Evidence Modeller, but couldn't succeed, Evigan was not working well with multifasta file (assembled contig file) and Evidence Modeller creating issues with the number of directories it produces on "Partition " step. is their any other user friendly software to do this or can any one give the detailed installation steps of GLEAN or how do i work with multifasta in Evigan and Evidence modeller or any other software.

          ......m stuck.........please Help

          Comment

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