Thank you very much...I will tell you briefly about my project

based on the literature survey for my project I could find that the first intron of genes consist set of cis- regulatory elements(cis- regulatory elements are small stretch of DNA sequences) such as TATA box, CAAT box, GC box. when consider the importance of such elements, they are involve in transcription regulation. In this case I thought to find out patterns of such cis-elements in first intron. in this case I would like to select housekeeping(HK) genes ,Tissue Specific genes(TSP) and most importantly functionally related (co-expressed) genes.

I have Already down loaded the first intron of Both HK and TSP genes. So that in order to get start I need advice for example I have a problem how can I use such sequence(cis-element) for feature vector, what kind of algorithm do I need to use...etc

I am very happy if you can give me some guidance. for sure this is not for fulfill home work..I need to learn this and how to I implement this for my future career...so that I need a point to start this then I can continue...I hope you may guide me

thank you