Thursday, April 16, 2009

Is it a bad thing ...

... if I know the MCS sequence of pCR4-TOPO by heart?

Manually sorting through over a dozen 96 well plates of sequencing is a pain in the toosh. I'm dreading what's going to happen when I need to submit all of this to GenBank. Fortunately for me, it's mostly a descriptive study of a site, so I can probably get away with submitting it as an aligned environmental set!

6 comments:

Anonymous said...

I'm curious where you get your sequencing done. we just started using Washington University and are pretty happy with it, cheap and easy for sure!

why the manual sort rather than use Geneious?

Thomas Joseph said...

Large scale projects are done with a collaborator within our agency. For small scale stuff we need immediately, we use MCLab. They do great work and very quick turnaround. I highly recommend them.

I do use Geneious, but while they have algorithms for screening vector that works great from the 5' end it's hit of miss coming from the 3' end sometimes. So I always go through manually (usually after aligning to make things a bit quicker) even if it's just to clean up the N's prior to submission.

Mad Hatter said...

Yes, that's totally fucked up. But for what it's worth, not anymore fucked up than of the rest of us!

BTW, I'm currently having a little disagreement with the GenBank submission people on how I annotated my sequences. Hope your process goes more smoothly than mine.

Anonymous said...

I tried the vector screen on geneious and found it didn't work so well, so I ended up just searching for motifs of my primers then manually trimming off anything outside my the insert region. It seems like there's got to be a better way, but I haven't figured it out.

Thomas Joseph said...

Perhaps you could fire them off an email. They're really good at getting back in touch with you. Maybe we're both just doing the vector screening wrong? When I get a chance, I'll look into it a bit more.

Thomas Joseph said...

Just an FYI: Just installed the latest version of Geneious (4.6.1) and its vector/trim ends function is a lot more robust than the prior version. You should see a big improvement.