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Gene identification, Fgenesh gene finder and Fgenesh++ genome annotation pipeline, 42 custom made gene-finding parameters. Largest Plant Gene Regulatory Elements database RegSite (~ 3000 entries).
FGENESH - Program for predicting multiple genes in genomic DNA sequences . FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et al.
Fgenesh - most accurate and fastest HMM-based gene prediction program; Fgenesh+ - gene prediction program that uses similar protein information; gene finding parameters for Fgenesh and Fgenesh+;
This is a list of software tools and web portals used for gene prediction. Its name stands for Prokaryotic Dynamic Programming Genefinding Algorithm. It is based on log-likelihood functions and does not use Hidden or Interpolated Markov Models. The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome.
FGENESV is the fastest ab initio viral gene prediction program available. We developed new FGENESV-Annotator script that finds similar proteins in public databases and annotates predicted genes. This script can also identify low scoring genes if they have known homologous protein.
Fgenesh++ is a bioinformatics pipeline for automatic prediction of genes in eukaryotic genomes. It can produce fully automated genome annotations of a quality similar to manual annotation, and is extremely fast compared to some other automated genome annotation pipelines.
Fgenesh+ was developed to analyse sequences from human, drosophila, nematode and plant, as well related organisms. The program can be used if you know protein sequence similar to protein which is predicted for a gene in your sequence. First, run any ab initio gene finding program such as Fgenes or Fgenesh.
