Sequence Databases

juggernaut4 · Post by **juggernaut4** » Tue Aug 14, 2007 3:51 pm

Hello!

I have a very strange question regarding bioinformatics projects. I am trying to continue a project from last year on bioinformatics, but I don't think I can if I have this problem. Basically, I'm comparing genic and intergenic sequences. However, since not all genes have been identified, couldn't intergenic sequences in the databases potentially be genic?? And then, you would never know FOR SURE whether your intergenic sequence is truly intergenic, or merely an unidentified genic segment?

If this question needs clarifying, please let me know. Thanks!

juggernaut

Lise Byrd · Post by **Lise Byrd** » Sat Aug 18, 2007 2:39 pm

Juggernaut,

You are right that your question is complex. We certainly have not identified all genes. Furthermore, genes can come from the same segment of DNA but opposite strands (these are called sense-antisense genes), and different RNAs can derive from overlapping sequences on the same DNA strand.

Have you decided the organism you will be using to explore genic/ intergenic sequences? For many model organisms (for example, japonica and indica rices and Arabidopsis thaliana), you can find databases that contain DNA sequences, RNA sequences, and cDNA sequences. You may be able to refine your question by choosing certain sequences (such as mRNA or cDNA) to represent "genic" segments.

I hope this helps. Post back if you have more questions.
Sonia

juggernaut4 · Post by **juggernaut4** » Sat Aug 25, 2007 6:38 pm

Thank you, that really has helped! I think I will just do the experiment on humans, however. thanks again,

juggernaut