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.
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|
- Gene Prediction Page on Wikipedia HERE
First of all, let me clear it that i am not a Bioinformatician. i am simple plant biology researcher who face problem in her daily research life and who bother to post solution of those problem on this webpage. That's it.