new at this and need some guidance

[DataDiviner]

Hi all,
I am new at this so I hope I am posting in the right section.
I am building a tool that compares transcriptomes of the same species. What I think that ends up meaning is comparing the RNA sequences. I am building the tool in java and looking to compare the two sequences somehow. My first guess was to try to align them then compare the differences in some way. Any suggestions or places to look or things to think about would be greatly appreciated. Thanks!

[pmiguel]

Hi DataDiviner,
Two sequences? A typical "transcriptome" will comprise >30 million reads per sample these days.

I would recommend that you leave this part of the problem to the programmers that have been hammering on it for 5 years now. Why not look farther downstream? After read assembly into a transcriptome using some program (eg, Trinity, etc.), you may be able to create some tool to analyze the presence/absence of enzymes in a given biochemical pathway as predicted by the presence/absence of RNA transcripts encoding those enzymes.

This seems like a much more tractable problem, yet one only sparsely addressed by the suites of available software now available. You could start by solving the problem for some particular pathway in your species of interest and then generalize it to other pathways/other species, if it works out.

--
Phillip

[DataDiviner]

Thanks! I'll try through this avenue!