Wildlife Biologist interested in Sequencing

[jpleonard2000]

Hello Everyone,

I am a PhD student in Wildlife Biology at Texas A&M University-Kingsville. As part of my dissertation, I am planning to examine MHC diversity in some highly endangered and fragmented populations of ocelots.

At this point, I am trying to decide which sequencing method to use on my samples. We have an ABI 3130xL analyzer in the lab, which is probably sufficient for my purposes, but I'm not really looking forward to all that cloning.

I'm considering sending my samples in to a lab in order to have them sequenced on an IonTorrent PGM. Basically, it's going to come down to cost. I have a really small gene (238 bp) that I'm looking at, which can have up to 3 repeats per chromosome. If I can put unique barcode adapters on all my samples and multiplex them together that would be a lot easier than doing things the old school way. If anyone has any thoughts about this I'd love to hear them. This is a new field for me.

[JackieBadger]

You're stepping in to a very very very dark place!
ha..
There are a few published protocols out at the moment (and another on the way) that uses 454 sequencing. And for your amplicon size 454 will work... but...bang for your buck?? 454 doesnt come close to alternative technologies.

We have a new MHC genotype protocol that will be coming out this year...It has been almost 3 years in the making, because believe me there have been A LOT of unforeseen hurdles along the way to the ignorant PhD student i.e. me...If you email me we can discuss how to go about your project, and potential in collaborating (we have a next gen sequencer)
[email protected]