Problem Solving Task- All help appreciated!

[PFitch]

While I realise this isnt the purpose of the forum per se, I thought the members here would be best suited to offer me any help regarding this issue:


I have been set a problem solving task as college work, and I have a few ideas about how to go about it but would like any input!

The objective of the exercise is to create a map of a DNA sequence showing the position of genes and any other features that you consider to be of interest

it is a very short sequence, around 12kb-

I have used ORF finders to identify the start zones of possible genes, and BLAST searched the immediate sequence following. It is relatively easy to identify genes within the sequences but I would like any advice on how I can identify other areas of interest.

I havent included the sequence because I don't want this done for me, just some guidance on direction I could take.

Thank you all for your help!

[ECO]

As much as I'm hesitant to help with your homework...you offered some evidence of thinking about it first.

I'd think about looking for secondary structures, repeat elements, repeated segments (self homologous regions)...

[HESmith]

For ideas about the types of elements that might be present, you might check out the modENCODE project. Note that they identify functional elements experimentally rather than computationally, but informatics tools exist for some of them.