Table 8. Genome Browsers and Tools for Gene Predictions and Feature Finding
Genome Browsers
Program Website Comments
UCSC http://genome.ucsc.edu Fast, interactive display of genomes. BLAT alignment tool
Ensembl http://www.ensembl.org Maintains automatic annotation of genomes. Interactive display of annotations
NCBI http://www.ncbi.nlm.nih.gov/mapview/ Maintains automatic annotation of genomes. Interactive display of annotations
Mapping of Sequences to Genomic DNA
Program Website Comments
BLAT http://www.genome.ucsc.edu/cgi-bin/hgBlat Fast alignment & chromosomal mapping of nucleotides/proteins to genomes
Est2Genome http://bioweb.pasteur.fr/seqanal/interfaces/est2genome.html Aligns spliced transcribts (EST & mRNA) to genomic DNA
Sim4 http://pbil.univ-lyon1.fr/sim4.php Aligns spliced transcribts (EST & mRNA) to genomic DNA
Spidey http://www.ncbi.nlm.nih.gov/IEB/Research/Ostell/Spidey/ Aligns spliced transcribts (EST & mRNA) to genomic DNA
Intron/Exon Predicitions
Program Website Comments
ORF Finder http://www.ncbi.nih.gov/gorf/gorf.html


 		 Finds all open reading frames. Graphical analysis tool
Diogenes http://www.cbc.umn.edu/diogenes/diogenes.html Finds all open reading frames (in short genomic sequences)
Metagene http://www.rgd.mcw.edu/METAGENE/ Exhaustive analysis of gene features from 7 prediction servers
NetGene2 http://www.cbs.dtu.dk/services/NetGene2/ Predicts splice sites in Humans & C. elegans DNA (Neural network)
HMMGene http://www.cbs.dtu.dk/services/HMMgene/ Predicts genes in vertebrate & C. elegans (HMM-based method)
FirstEF http://rulai.cshl.org/tools/FirstEF/ First exon prediction
Gene Prediction Tools
Program Website Comments
GeneMark http://opal.biology.gatech.edu/GeneMark/ Multiple gene prediction programs. Eukaryotic genefinding
GenScan http://genes.mit.edu/GENSCAN.html Eukaryotic genefinding (HMM-based method)
GenomeScan http://genes.mit.edu/genomescan.html Incorporates homology data in gene prediction
GrailEXP http://compbio.ornl.gov/grailexp/ Gene finding incorporating ESTs, exon prediction & promoter/polyA recognition
Glimmer http://www.tigr.org/softlab/glimmer/glimmer.html Finds genes in microbial DNA (genomes of bacteria and archaea)
GeneFinder http://www.bioscience.org/urllists/genefind.htm Rule-based identification of features, including codon bias
TwinScan http://genes.cs.wustl.edu/ Use genome comparison (human mouse conservation) and statistical patterns
Genie http://www.fruitfly.org/seq_tools/genie.html Trained for fly and other invertebrate organisms
SGP http://kiwi.ice.mpg.de/sgp-1/ Use genome comparison, exons predicted in both sequences
FGENESH http://www.softberry.com/berry.phtml Suite of gene finding tools (pattern based). Highly accurate
HMMgene http://www.cbs.dtu.dk/services/HMMgene/
 		 Prediction of vertebrate genes
Polyadq http://rulai.cshl.org/tools/polyadq/polyadq_form.html Detection of polyadenylation signals
Promoter Prediction
Program Website Comments
Zhang Lab http://rulai.cshl.org/software/index1.htm



 		 List of some promoter resources
BDGP http://www.fruitfly.org/seq_tools/promoter.html Neural network promoter prediction
TATA-box http://wwwmgs.bionet.nsc.ru/mgs/programs/bdna/tata_bdna.html Finds TATA-boxes
TRANSFAC http://www.gene-regulation.com/ Transcription factor database
Gene Indices and EST Databases
Program Website Comments
Unigene http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene Gene-oriented clusters of all Genbank sequences (ESTs and cDNAs)
TIGR http://www.tigr.org/tdb/tgi/ Gene-oriented, organism-specific clusters of ESTs and cDNAs
dbEST http://www.ncbi.nlm.nih.gov/dbEST/index.html Large database of raw, partial cDNA sequences from a number of organisms
Gene2EST http://woody.embl-heidelberg.de/gene2est/ A BLAST server for searching EST databases with genomic DNA
SAGE http://www.sagenet.org/ Analysis of gene expression patterns based on ESTs
Alternative Splicing Databases
Program Website Comments
ASAP http://www.bioinformatics.ucla.edu/ASAP/ Alternate splicing analysis tool
HASDB http://www.bioinformatics.ucla.edu/%7Esplice/HASDB/ Human alternative splicing database
AsMamDB http://166.111.30.65/ASMAMDB.shtml Alternatively spliced genes in human, mouse and rat
ASD http://cgsigma.cshl.org/new_alt_exon_db2/ Alternative splicing database at Cold Spring Harbor Laboratory
EASED http://eased.bioinf.mdc-berlin.de/cgi-bin/search Extended alternatively spliced EST database
BDGP http://www.fruitfly.org/seq_tools/splice.html Splice site prediction (Neural network)
Comparative Genomic Visualization Tools
Program Website Comments
VISTA http://www-gsd.lbl.gov/vista/ Suite of programs for comparative analysis of genomic sequences
PIPMaker http://bio.cse.psu.edu/pipmaker/ Visualizes relationships among two or more DNA sequences