Table 8. Genome Browsers and Tools for Gene Predictions and Feature Finding
Genome Browsers
Program Website Comments
UCSC Fast, interactive display of genomes. BLAT alignment tool
Ensembl Maintains automatic annotation of genomes. Interactive display of annotations
NCBI Maintains automatic annotation of genomes. Interactive display of annotations
Mapping of Sequences to Genomic DNA
Program Website Comments
BLAT Fast alignment & chromosomal mapping of nucleotides/proteins to genomes
Est2Genome Aligns spliced transcribts (EST & mRNA) to genomic DNA
Sim4 Aligns spliced transcribts (EST & mRNA) to genomic DNA
Spidey Aligns spliced transcribts (EST & mRNA) to genomic DNA
Intron/Exon Predicitions
Program Website Comments
ORF Finder

Finds all open reading frames. Graphical analysis tool
Diogenes Finds all open reading frames (in short genomic sequences)
Metagene Exhaustive analysis of gene features from 7 prediction servers
NetGene2 Predicts splice sites in Humans & C. elegans DNA (Neural network)
HMMGene Predicts genes in vertebrate & C. elegans (HMM-based method)
FirstEF First exon prediction
Gene Prediction Tools
Program Website Comments
GeneMark Multiple gene prediction programs. Eukaryotic genefinding
GenScan Eukaryotic genefinding (HMM-based method)
GenomeScan Incorporates homology data in gene prediction
GrailEXP Gene finding incorporating ESTs, exon prediction & promoter/polyA recognition
Glimmer Finds genes in microbial DNA (genomes of bacteria and archaea)
GeneFinder Rule-based identification of features, including codon bias
TwinScan Use genome comparison (human mouse conservation) and statistical patterns
Genie Trained for fly and other invertebrate organisms
SGP Use genome comparison, exons predicted in both sequences
FGENESH Suite of gene finding tools (pattern based). Highly accurate
Prediction of vertebrate genes
Polyadq Detection of polyadenylation signals
Promoter Prediction
Program Website Comments
Zhang Lab

List of some promoter resources
BDGP Neural network promoter prediction
TATA-box Finds TATA-boxes
TRANSFAC Transcription factor database
Gene Indices and EST Databases
Program Website Comments
Unigene Gene-oriented clusters of all Genbank sequences (ESTs and cDNAs)
TIGR Gene-oriented, organism-specific clusters of ESTs and cDNAs
dbEST Large database of raw, partial cDNA sequences from a number of organisms
Gene2EST A BLAST server for searching EST databases with genomic DNA
SAGE Analysis of gene expression patterns based on ESTs
Alternative Splicing Databases
Program Website Comments
ASAP Alternate splicing analysis tool
HASDB Human alternative splicing database
AsMamDB Alternatively spliced genes in human, mouse and rat
ASD Alternative splicing database at Cold Spring Harbor Laboratory
EASED Extended alternatively spliced EST database
BDGP Splice site prediction (Neural network)
Comparative Genomic Visualization Tools
Program Website Comments
VISTA Suite of programs for comparative analysis of genomic sequences
PIPMaker Visualizes relationships among two or more DNA sequences