The ultimateTools for phylogenetic footprinting purposes
Transcription factor binding site detection using phylogenetic footprinting
Alignment and exon prediction in orthologous nucleotide sequences
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Genomic alignment / exon detection /gene finding
General genomic sequence analysis tools Genomic databases
Transcription factor site prediction
Pipmaker Aligns two DNA sequences, returns alignment and percent identity plot PromotorInspector Predicts promotor localization on a genomic sequence Ensembl (human) Annotated public human sequencing effort ConSite Transcription factor binding site detection using phylogenetic footprinting
Orthoseq Alignment and exon prediction in orthologous nucleotide sequences RepeatMasker screens DNA sequences against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions. Ensembl (mouse) Annotated public mouse sequencing effort
ClustalW Standard tool for multiple sequence alignment CpG CpG islands prediction Gene portals Pattern finding
Glass Alignment of orthologous genomic sequences
Genelynx
Portal to the human genome Meme/Mast Motif Discovery and Search
SGP1 Exon prediction based on sequence comparison Flybase Comprehensive gene portal for Drosophila Gibbs Motif Sampler Motif identification in DNA or protein sequences
GenScan Ab initio prediction of locations of exon-intro structures in genomic sequence Wormbase Comprehensive gene portal for C.elegans and closely related nematodes Anspec
Grail Gene recognitin and assembly Tair Comprehensive gene portal for A. thaliana Splice signal detection
GeneID Ab initio prediction of locations of exon-intro structures in genomic sequence Netgene2 Neural network predictions of splice sites in human, C. elegans and A. thaliana DNA
Rosetta Human exon prediction based on orthologous sequence comparison
Twinscan Human exon prediction based on orthologous sequence comparison
Dotter Graphical dotplot program for detailed comparison of two sequences
HMMgene 1.1 Prediction of vertebrate and C. elegans genes
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