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Checking which gene coding region prediction works for which eukaryotic genome

I am working on a project in which I plan to apply hidden markov models, fourier analysis method and super entropy method to find the gene coding regions in various eukaryotic genomes and then use some sort of clusturing to group the organisms on the basis of the method which worked bwst for them . For this I want to ask the following questions:

  1. Does some research exist related to the above.
  2. I am planning to use 200 eukaryotic genomes. Can anyone suggest me how to download the files from NCBI server (I am not able to understand from which directories to download which files. I need the complete genome and the gene coding regions as well. I plan to write a script for downloading.)

P.s: I am new to bioinformatics and this is my first question on biostar.

Thanks in advance

genome gene-prediction
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updated by Ram Ram • written by sainideepak119 • sainideepak119
  1. Yes it does, google for gene prediction eukaryotes, MAKER, augustus, snap, genemark, etc. and you will find all the prior art and software. https://en.wikipedia.org/wiki/List_of_gene_prediction_software Eukaryote gene prediction requires good training sets, I recommend that you read some review papers before deciding if and how to carry out such a project, this is imo not suitable for a beginner in bioinformatics.
  2. You need to consult the documentation of the NCBI FTP server
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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

Thanks for the info Michael. I guess biostars has rules similar to stack overflow. :)

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written by sainideepak119 • sainideepak119

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