Weeder

For finding over-represented sequence motifs in nucleotide sequences, tailored for finding Transcription Factor Binding Sites in sequences from co-regulated or co-expressed genes, or derived from large scale ChIP on Chip or ChIP Seq.

Web Interface and source code download

 

Pscan

Same as above, but it uses descriptors of binding specificity of known transcription factors. I.e., it looks for over-represented motifs according to TRANSFAC and JASPAR matrices.

Web Interface and source code download

 

WeederH

for finding of conserved nucleotide motifs and regions through comparative genomics, tailored for the analysis of non-coding DNA and the identification of conserved TFBSs or whole enhancers or silencers.

Web Interface and source code download

 

Exalign

for aligning gene intron exon structures, and performing BLAST-like database searches based on structural similarity.

Web Interface and source code download

 

RNAProfile

for finding motifs conserved in sequence and secondary structure in RNA sequences.

Source code download

 

GeneSyn

for finding conserved gene order throughout multiple genomes

Source code download