Cross-species TF scanner
Compare orthologous promoters for one gene across two or three species, in the spirit of ConTra (Kreft et al., NAR 2017). Promoters are fetched from NCBI (same symbol per species), grouped by transcription start site (TSS), aligned, then scanned for transcription factor binding sites on the reference species using the same MEME/JASPAR library as the TF binding scanner. Promoters are aligned with a threaded blockset method inspired by TBA/MULTIZ (Blanchette et al., 2004): locally homologous blocks are chained on the reference sequence; divergent flanks stay unaligned instead of being forced into one global MSA.
High-stringency hits on the reference are tested for nucleotide conservation of the binding interval (± a few alignment columns) in the other two species. Use Promoter Grabber to inspect a single species in more detail.
Max 1,000 bp promoter per species (5′ + into gene).
TBA-lite finds local homology blocks via k-mer seeds (like BLASTZ/MULTIZ), projects them onto the reference, and leaves non-homologous promoter sequence unaligned in other species.
Transcripts are grouped when genomic TSS positions differ by ≤10 bp. Choose one group per species (promoter TSS uses the most common position in the group, or the average if tied).
Reference species
Species 2
Species 3
| block boundary · yellow gaps = no homology in that species for this reference interval