Aligning to different regions with BWA

[shmibble]

Hi,
I was wondering if it is possible in BWA (or perhaps a similar program) to use a reference sequence composed of several different regions. For example if I have several genes which I would like to use. So basically a non-contiguous reference sequence.
Is there a way to do this without aligning separately to each region? And if so how?

Thanks for any advice!

[Brian Bushnell]

Concatenate all of them into a single fasta file and use that as the reference. For example:

>region_1
ACGTGT...
>region_2
GGCCTG...

...etc.

[shmibble]

Perfect. Many thanks!