Fgenesh+

Input
Sequences Set your source file with nucleotide sequences in FASTA format.
Homologous Sequence(s) Set your source file with homologous sequences in FASTA format.
Organism Parameter file for specified organizm.
Output
Result Name of the output file.
Print mRNA Enabling this option results in output the nucleotide sequences of all predicted exons separately.
Print Exons Enabling this option results in output the nucleotide sequences of all predicted exons separately.
Threshold for Flanking Exons This option specifies the minimal allowed length for flanking exons, which has no similarity with homologous sequence, to output.
Options
Minimal Exon Homology Exon is considered as completely unsimilar, if its similarity with the homologue is less than the value specified (in percents).
Costs for Exons Homology: Costs for Exons Homology:
  • Exons Homology Bonus
    • - If a potential exon has a similarity with given homolog, its resulting score will be equal to intial score plus the score of homology multiplied by the set value.
  • Penalty for Non-Homologous Exons
    • - This option specifies a penalty for the internal predicted exons, which have no similarity to homologue and lie between the exons possessing homology.
    Use GC donor splice sites: Use GC donor splice sites:
  • Use all potential GC sites
    • - Use all potential GC donor sites.
  • Set Threshold
    • - Use potential GC donor splice sites with score higher the current value only.
    Set Search Range Set Search Range:
  • Starting Position
    • - Set the starting position for search region in sequence.When this option is not checked, the programs uses the first nucleotide as starting one.
  • Ending Position
    • - Set the ending position for search region in sequence.
    Alternative Variants Output: Alternative Variants Output
  • Output Variants Number
    • - Set the maximal number of best alternative prediction variants to output.
  • Variants Skipping Threshold
    • - Set the scoring threshold for the program to skip variants of prediction with score lower than the set portion of the best prediction score. I.e. if the value is set to 0.75, and the best prediction score is 1000, then all variants with score lower than 750 will be ignored.
  • Number of Best Exons to Include
    • - Force the program to include in alternative prediction variants the set number of best exons, which were not initially included in the best prediction, sequentially. This means the program makes a prediction with the best score, after which some potential exons with high score remain unincluded in this prediction. Enabling this options forces the program to generate alternative variants that must contain the set number of these exons.
  • Number of Best Sites to Include
    • - Force the program to include in alternative prediction variants the set number of exons with good splicing sites, which were not initially included in the best prediction, sequentially. This means the program makes a prediction with the best score, after which some potential exons with good splicing sites remain unincluded in this prediction. Enabling this options forces the program to generate alternative variants that must contain the set number of these exons.
  • Stop Exons Skipping
    • - By default the program makes the best prediction and then tries to generate alternative variants sequentially skipping the exons, which were included in this prediction. Enabling this option prevents using this method.
    Allow to Skip Promotors During the check, for each potential promoter two alternative variants are considered:
    1. The promoter is included in gene structure with formation the following 5'UTR upstream the CDS;
    2. The promoter is not considered in gene structure, and predicted sequence begins directly with CDS (1st exon).
    Enabling this option allows both variants with following choosing of the best prediction.
    Allow to Skip Terminators During the check, for each potential terminator two alternative variants are considered:
    1. The terminator is included in gene structure with formation the previous 3'UTR downstream the CDS;
    2. The terminator is not considered in gene structure, and predicted sequence ends directly with CDS (last exon).
    Enabling this option allows both variants with following choosing of the best prediction.
    Exons Restrictions Exons Restrictions:
  • First Exon Minimum
    • - Set the minimal allowed length for the first exon.
  • Internal Exon Minimum
    • - Set the minimal allowed length for the internal exon.
  • Single Exon Minimum
    • - Set the minimal allowed length for the single exon.
  • Terminal Exon Minimum
    • - Set the minimal allowed length for the terminal exon.
  • Exons Skipping Threshold
    • - Set the scoring threshold for the program to skip potential exons with score lower than the current one.
    Specificity Factor Set the specificity of algorithm (from -10 (High) to +10 (Low)).
    Increasing the parameter value results in increased number of predicted "True" exons, but the number of predicted "False" exons is also being increased. Generally, increasing of false exons prediction is drastically greater than increasing of true ones.
    Decreasing the parameter value results in symmetric situation with decreasing of predictions number.