5 Server for Gene Prediction from Plant Genome

Now a  Day, gene prediction tools are another important tools which are utilizing by different researchers to find out the open reading frame in vast amount of sequence data. One of Bioinformatics-made-Simple reader asked me to give a list of few tools for plant gene prediction. 

Also read

At Eukaryotic GeneMark.hmm you can predicts ORFs from several number of eukaryotic genomes. You can follow the steps given in Figure 1. Select the file  containing sequence (Step 1), select the genome name (Step 2) and finally select the output type (Step 3)

Figure 1 : Plant gene prediction by  GeneMark.hmm    
FGENESH is a server from SoftBerry. FGENESH is also have a good collection of genome to predit the gene from. Follow the steps given in figure 2.
Figure 2 : ORF prediction by FGENESH

GENESCAN is a webserver hosted at MIT. It has Limited genomes bu bit fast server. Steps to use GENESCAN are given in figure 3.

Figure 3. Gene prediction by GENESCAN
GeneSeqer is hosted on PlantGDB dedicated to plant genomes. Although it is a good Bioinformatic server bu bit slow. Steps to use GeneSeqer is given on their webpage.

Geneid is my favorite server for gene prediction. Beside their good collection of genome specific ORF finder, fast speed, Geneid's capability to predict the gene from multiple sequence is my favorite feature. Although, I have not use it for large file but a file with three sequence (Size > 100 kb) was predicted successful. You can use different output formats also. First give your sequence, choose your genomes (Step 1, Figure 4), choose the mode to execute the software  (Step 2, Figure 4), way of prediction of gene on DNA strand   (Step 3, Figure 4)

Figure 4 : First phase of  gene prediction from Geneid

In second phase of ORF prediction by Geneid, you will choose the output format and other important feature of gene in your result file (Figure 5).

Figure 5 : Second phase of  gene prediction from Geneid 
Further Reading

  1. Gene Prediction Page on Wikipedia  HERE


  1. Thank you once again for the information gene prediction tools. I tried FGENESH and got the out put and try to convert into gff file using the perl program cnv_fgenesh2gff.pl ( got from web) it throwing error no such directory and making the input file zero bytes .
    I am not a perl programmer but can run the readily available progrms. I request you to suggest something to make the fgenesh out put in a tabular form so that it can be used further. the output table should contain inputseqno. details (i.e tss/5utr/exon/intron/3utr/polyA/intergenic); start and end length fields.
    Once again Thank you for the prompt response.

    1. Actually those perl script depends upon several perl modules so it's difficult to sort out the problem. However, hope this will help for you

      How to Predict Gene from Multiple Sequence


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