• 1. AGenDA
• AGenDA is a gene-prediction tool that is based on cross-species sequence comparison. The software tools CHAOS and DIALIGN are used to align a pair of syntenic genomic sequences, e.g. from human and mouse. AGenDA searches for conserved splice sites and start/stop codons at the boundaries of identified sequence homologies in order to identify potential exons.

• 2. Augustus: gene prediction
• Univ. of Gottingen. AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

• 3. BDGP: Neural Network Promoter Prediction
• Lawrence Berkeley National Laboratory. Uses neural network programming techniques to predict promoters from a submitted sequence

• 4. CPC - Coding Potential Calculator
• Peking University. CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.

• 5. EasyGene 1.2 Server
• BINF, Copenhagen. EasyGene 1.2 server uses HMM to produce a list of predicted genes given a sequence of prokaryotic DNA.

• 6. FrameD
• FrameD locates genes and frameshifts in procaryotic sequences and matured eukaryotic sequences (to predict and correct frameshifts in EST, EST clusters and cDNAs).

• 7. Gene Finder
• Cold Spring Harbor. This page contains software tools designed to predict putative internal protein coding exons in genomic DNA sequences for humans, arabidopsis, yeast and mice.

• 8. GeneAlign
• GeneAlign is a gene prediction tool that uses conservation of gene structures and sequence homologies between protein coding regions to increase prediction accuracy. GeneAlign is currently configured to align human and mouse sequences for gene prediction.

• 9. GENSCAN Web Server at MIT
• MIT. Scans a DNA sequence for promoters and predicts gene make-up

• 10. GrailEXP
• GrailEXP is a software package that predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements within DNA sequence.

• 11. HomoloGene
• NCBI. HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.

• 12. IBM Bioinformatics and Pattern Discovery Group
• A suite of IBM bioinformatics tools that perform gene prediction,sequence pattern analysis and text searching

• 13. ORF Finder
• NCBI. The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database.

• 14. OrfPredictor
• Fungal Genomics Project. Prediction of Open Reading Frames (ORFs) and coding regions of a batch of EST or cDNA sequences.