Bioinformatics method to find which genes have GC and TATA boxes ?

Question

[shome]

I can manually check out if a gene has GC or TATA box. But, are there any suggestions for bioinformatics software/methods to find if a long list of genes has a GC/TATA box or not?

Answer 1

[Mensur Dlakic]

The list of programs that can search for DNA motifs is very long, as this is one of the earliest applications of bioinformatics. Just about any motif finder has companion programs that can do motif scanning as well. Beware that DNA motifs such as the initiator binding site and TATA-box are very short, and therefore can be found in many spots in genome that are not promoters. For example, TATA-box is expected to occur randomly every 256 bp, and I am sure you realize that gene frequency is nowhere near once in every 256 bp.

• http://meme-suite.org/tools/meme
• http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html
• http://homes.esat.kuleuven.be/~sistawww/bioi/thijs/Work/MotifSampler.html
• https://bammmotif.soedinglab.org/
• https://en.wikipedia.org/wiki/Multiple_EM_for_Motif_Elicitation
• https://en.wikipedia.org/wiki/Sequence_motif
• https://molbiol-tools.ca/Motifs.htm
• https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-S7-S21