Okay, so my mom wants a new desktop for the office. She currently has an old pentium D (that's right, TWO Prescott dies on one chip

). I currently have an athlon 64 x2 7750BE (2.7ghz) with 4gb ddr2 ram and a radeon hd 4650, and until lately it's been doing me just fine (I mostly just use my laptop out of laziness).
However, I've started doing some pretty intense research in bionformatics now that I'm in grad school, and the programs I write to process data (despite achieving the best possible efficiency and time complexity) are very very CPU intensive. We're talking average run times of WEEKS here. So, as you can imagine anything that can speed up the process is very much appreciated (the university servers are hopelessly overloaded, or I would use them instead).
To that end, I suggested to my mom that for around $700 I can put together a brand new rig with a phenom II X6 1090T black edition and 4gb of ddr3 1333, and then just give her my old one and have the business reimburse me the $700.
The thing is, though, that she won't be needing anything more than integrated graphics, so I'm trying to decide whether or not to just keep the radeon hd 4650 for myself or upgrade it. As I said, the things I'm doing on it are intensely CPU-bound, and unfortunately it's an inherently linear problem (you don't see too many of those outside research, but they're more common than you think in academia), meaning that there really isn't any benefit from multithreading or GPU computing (besides, I would probably shoot myself before I'd rewrite all my code in C to run it on a GPU

), aside from running several instances of the program in parallel.
I will probably eventually be gaming on it, but I've kinda grown out of it at this point (no time these days

), and besides, it's going to be tied up for the next year and a half just crunching numbers.
So do you think it's worth it to upgrade the video card? I've taken a look at the hd 6450, for example, and it actually seems LESS powerful than the 4650 (less SPUs, less shaders, etc.).