MAKER Test

MAKER is a genome annotation pipeline[1]. It allows for a researcher or group of researchers to take a genome, some amount of evidence (for example, an EST file, a protein file (both in FASTA format), and a repeat file, and potentially more), and create structural annotations for a genome. It is capable of training HMM files in order to provide better annotations for a genome with little evidence, although this takes many runs. This page is an attempt to document the work being done to add MAKER into CoGe.

How to Download and Install MAKER

MAKER may be downloaded from the Yandell lab, here: http://www.yandell-lab.org/software/maker.html. The full installation instructions may be found here: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial. The instructions here will just serve as a brief overview for getting MAKER running on the command line in UNIX.

1. Register and download MAKER from the Yandell lab MAKER software page. 2. Unpack MAKER in whichever folder it will be run from. 3. Download and install prerequisites if they are not installed. The minimum prerequisites are:

    a. BioPerl and various other Perl modules (see the MAKER documentation for a complete list[2]).
    b. SNAP
    c. Exonerate
    d. RepeatMasker
    e. NCBI BLAST

4. Add MAKER and its prerequisites to $PATH. For example, the paths might look something like:

    a. MAKER: export PATH="/home/user/maker/bin:$PATH"
    b. RepeatMasker: export PATH="/home/user/RepeatMasker:$PATH"
    c. Exonerate: export PATH="/home/user/exonerate-2.2.0-x86_64/bin:$PATH"
    d. SNAP: export PATH="/home/user/snap:$PATH"

5. Set up the MAKER control files by typing "maker -CTL". 6. Open the MAKER boot options file ("maker_bopts.ctl") and ensure that the correct BLAST search type is selected.

    a. For example, to use NCBI-BLAST, set "blast_type=ncbi+".

7. Edit the MAKER options file ("maker_opts.ctl") to the desired settings.

    a. To set the genome, enter the path to the genome after "genome=". So, this might look like "genome=dpp_contig.fasta". Leave a space between this and the commented description (which starts with a "#" symbol).
    b. Set the EST or mRNA data by typing the path to the desired EST or mRNA fasta file after "est=".
    c. To have MAKER generate structural annotations directly from EST or mRNA data, change "est2genome=0" to "est2genome=1".
    d. Change any other desired settings. For more details on these settings and how to set them, see the full MAKER tutorial[3].

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