Science Buddies: "Ask an Expert"

Dear SciBuddies

Good day,

I am doing a science project with the local university which part of requires me to find transcriptional factors for six antioxidant enzymes and six protein kinases. Is there a particular bioinformatics protocol that I could be advised to follow to make things easier in order to pass this particular stage. My advisor told me about the Transfac database, but I was very confused on how to use it. If there is any bioinformatics advice I could be given, I would greatly appreciate it. My advisor once told me it involved things like polymol, heatmaps, molecular docking, BLAST and things like that. I am not very trained in this field and have read so much on it but I am a little lost on how to start things.

Thank you so much for your time and advice in advance,

Kind Regards,

Ryann,

Hello there!

Welcome to Science Buddies! What a cool project! Bioinformatics is really fun and super powerful.
Transcription Factors typically have a sequence motif that is associated with them: https://en.wikipedia.org/wiki/Sequence_motif
There are multiple software programs that you can use to identify transcription factors in the sequences you are investigating. You usually need to obtain a specific format of the sequence called a FASTA file. This looks something like this
>sequence_Name other information
AGTGATGCGTACACATCAC

Here is a web based program that looks for motifs. http://www.genome.jp/tools/motif/

I hope this helps you get started in the right direction. let me know if you have any more questions! I'm sure some other experts may have more to add as well