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gene_prediction_just_genemark [2023/07/07 14:28] – [GeneMark-ET] 134.190.232.186gene_prediction_just_genemark [2026/02/26 11:53] (current) – 129.173.242.70
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 ====== Gene prediction with just GeneMark ====== ====== Gene prediction with just GeneMark ======
  
-Joran Martijn (January 2023)+Created by Joran Martijn in 2023. 
 + 
 +Updated by Jason Shao on February 26th, 2026.
  
 **GeneMark** is one of oldest gene prediction tools still in development, with papers describing the first algorithms as early as [[http://exon.gatech.edu/Genemark/PDF/Statistical_Patterns_in_Primary___Article.pdf|1986]], [[https://www.sciencedirect.com/science/article/pii/030326479390068N|1993 (1)]], [[https://www.sciencedirect.com/science/article/pii/009784859385004V|1993 (2)]] and [[https://academic.oup.com/nar/article/26/4/1107/2902172?login=true|1998]]. The latest update (as of January 2023, GeneMark-EP+) has been published in [[https://academic.oup.com/nargab/article/2/2/lqaa026/5836691?login=true|2022]]. **GeneMark** is one of oldest gene prediction tools still in development, with papers describing the first algorithms as early as [[http://exon.gatech.edu/Genemark/PDF/Statistical_Patterns_in_Primary___Article.pdf|1986]], [[https://www.sciencedirect.com/science/article/pii/030326479390068N|1993 (1)]], [[https://www.sciencedirect.com/science/article/pii/009784859385004V|1993 (2)]] and [[https://academic.oup.com/nar/article/26/4/1107/2902172?login=true|1998]]. The latest update (as of January 2023, GeneMark-EP+) has been published in [[https://academic.oup.com/nargab/article/2/2/lqaa026/5836691?login=true|2022]].
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 This is perhaps the most straightforward and pure //ab initio// gene prediction tool. Only the genome FASTA file is provided, and the algorithm will do its best without any external sources of evidence or training input (hence Self-training), to predict the gene start and end locations, including possible introns. This is perhaps the most straightforward and pure //ab initio// gene prediction tool. Only the genome FASTA file is provided, and the algorithm will do its best without any external sources of evidence or training input (hence Self-training), to predict the gene start and end locations, including possible introns.
 +
 +Create a conda environment for GeneMark-ES:
 +
 +<code>
 +conda create -n genemark-es perl perl-mce perl-yaml perl-hash-merge perl-parallel-forkmanager
 +</code>
 +
 +Running GeneMark-ES:
  
 <code> <code>
 +source activate genemark-es
 gmes_petap.pl --sequence <genome.fasta> --ES gmes_petap.pl --sequence <genome.fasta> --ES
 </code> </code>
gene_prediction_just_genemark.1688750898.txt.gz · Last modified: by 134.190.232.186