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