Hi Sergio,

I am not sure what you exactly want but you may use IGV (https://igv.org/doc/desktop/) and has a version for every platform. OR you may try BLAST (stand alone in unix/linux) to run with multiple files. You have options to tweek your output (https://www.ncbi.nlm.nih.gov/books/NBK52640/).

Good luck.

Shajahan

Drar Sergio Fandiño González

visualize overlapping transcription factor binding sites (TFBS) in small promoter sequences, there are several tools that can offer more flexibility than CIIIDER, especially in scaling for smaller sequences. Here are a few options:

Geneious Prime:-

A versatile tool that can handle sequence visualization with great flexibility. It allows you to plot features like TFBS on promoters, and you can easily adjust the display settings (such as zoom level and layout) to accommodate small sequences. (Great for visualization, especially with smaller sequences, and you can customize the scale)

Jalview:-

While originally designed for sequence alignments, Jalview can also be adapted to visualize TFBS overlaps if formatted correctly. It's highly customizable, and you can import your sequence with annotations.(Free, open-source, and allows for extensive customization)

IGV (Integrative Genomics Viewer):-

Though mainly used for large-scale genomic data visualization, IGV can be adapted for small sequences like promoters. You can load your TFBS as bed files, and it will allow you to visualize the overlapping regions.

Good luck.

Yashavant

Hi Sergio,

I recommend Geneious Prime if you need more flexible software than CIIDER since you'll be working with smaller scales of DNA sequences. You can adjust and customise the settings to visualise the overlapping regions easily. Of course, other options like Snapgene, IGV, and ApE exist, but I'm not entirely familiar with those. All the best; I hope it helps!