Phylogenetic Footprinting

The ultimate Tools for phylogenetic foot printing purposes

 

 

 

Transcription factor binding site detection using phylogenetic footprinting

Alignment and exon prediction in orthologous nucleotide sequences

Our apologies for the recent server problems

 

Genomic alignment / exon detection /gene finding

 

General genomic sequence analysis tools Genomic databases

Transcription factor site prediction

 

 

  1. 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
  2. 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
  3. ClustalW Standard tool for multiple sequence alignment CpG CpG islands prediction Gene portals Pattern finding
  4. Glass Alignment of orthologous genomic sequences
  5. Genelynx
  6.  
  7. Portal to the human genome Meme/Mast Motif Discovery and Search
  8. SGP1 Exon prediction based on sequence comparison Flybase Comprehensive gene portal for Drosophila Gibbs Motif Sampler Motif identification in DNA or protein sequences
  9. 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
  10. Grail Gene recognitin and assembly Tair Comprehensive gene portal for A. thaliana Splice signal detection
  11. 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
  12. Rosetta Human exon prediction based on orthologous sequence comparison
  13. Twinscan Human exon prediction based on orthologous sequence comparison
  14. Dotter Graphical dotplot program for detailed comparison of two sequences
  15. HMMgene 1.1 Prediction of vertebrate and C. elegans genes

 

 

Sequence one (fasta file):
No file chosen

Sequence two (fasta file):

No file chosen

 

Output options:

DPB alignment (clustal format)

DPB blocks

exon prediction (gff format)

no plot

conservation plot

conservation plot showing predicted exons

 


Are you to Explore transcription factor binding sites shared by two genomic sequences

 

  1. Analyze orthologous pairs of genomic sequences
  2.  Analyze an existing alignment of genomic sequences
  3.  NEW/EXPERIMENTAL: Fetch genomic sequences of human:mouse orthologs by ID or keyword
  4.  Analyze single sequence