Hi, I'm a first time poster on this forum. I have a question regarding how to use Linux scripting so I can do pairwise protein analysis. I'm doing it by hand which is tedious and prone to many mistakes.

I want to have use program of some sort that will pick out identities and similarities under whatever limits I apply to it.

Is there anything out there already? If not, where can I start to make one myself? Thanks.

Have you performed a Google.com search?

I just tried a google search ... I know there are protein/dna/rna applications available, but I couldn't find anything decent. Problem probably is that i'm not sure what exactly to look for.

I'd suggest either a bash script which would enable you to go through ordinary text files (or perl or python if you'd prefer those).

Or perhaps set up a LAMP solution so you can have access to your data from anywhere you happen to have an internet connection at (if this is feasible).

Yea, but it's very limited and doesn't compare them the way I want to. They have their predetermined values and highlights sequences it in a pretermined way. I want to speed up the analyzing I'm doing since these won't programs will not catch subtle differences.

Do you work for a university or something for the research your doing? Perhaps you can have them fund you where you can hire a programmer to modify one of these already-made solutions to do your particular task at hand.

Are you just a hobbiest? Is this professional work? What's your available budget?

If you aren't experienced in bash scripting already, then you're going to have great difficulty coding a script like this in Bash. I'd suggest a C/C++ based application anyways, as it'd have speed and portability.

If you are able to lay down some money for your work, I have a friend who would probably work very cheap (around the $60-$120 range) quite affordable if your work is important to you.

On any account, this would be a very interesting application of Linux.
Good luck, regards

This might be a good place to start looking for already-existing software:
http://helix.nih.gov/apps/bioinfo/

You can look into Biobrew and Bioknoppix .

Bioknoppix sounds like a good idea ... try that to see if you like it. As it won't touch your host system, you can leave everything installed as is. Then, if you're happy with what you get and comfortable with the software environment, you can set up a machine with that (I know Knoppix offers to just install on the host, does Bioknoppix do that too?). At any rate, this CD should be an excellent tool to test drive without having to worry about much of anything. Give it a try! Right .... now.