Conversation between fresh-faced young Honours student and myself:
PFY: What primer design program should I use.
BK: Your brain and a pencil and paper. I haven't used a primer design program in over ten years.
PFY: Gosh. I didn't know they existed back then.
Cheeky sod.
Still, I shall have my revenge. I am trying to work out a way of forcing him to use the command-line sequence analysis tools (eh, EMBOSS, mainly) as opposed to all this funky GUI (and gooey) stuff that is nowhere near as powerful or customizable. Getting him to install Linux on his laptop might be a good first move, as that's probably easier than teaching him how to ssh in to my Mac. But before all that I shall have to persuade him that Microsoft Word is not a sequence editor and that .doc is not a sequence format.
Young in the ways of the Force, my young apprentice is.
(A quick Google threw up ftp://emboss.open-bio.org/pub/EMBOSS/windows and http://www.interactive-biosoftware.com/embosswin/embosswin.html . Anyone have any opinions on these?)
Comments
hehe, I remember the gradstudent doing her Masters asking me the same thing when I did my PhD... although sometimes the combinations of programs and knowledge can be very good (reed> repeat regions etc.) :)
I haven't used the Emboss on a PC ever but I think the ftp address looks very interesting since that is done by Emboss themselves... I would have like that in contrast to having to make a partion of the hard drive, install win 98 with a dos prompt and then run the magnificent program pcgene ;) But hey, it worked really well and it saved the sequences in a real sequence format so I could then move on into emboss' world.
Good luck with it all! And maybe you need to teach the student some linux? I guess staden won't be a program he/she would use though? *evil giggle* but seing problems with seq format probably means no knowledge of linux/unix commands...
Posted by: challenge | March 1, 2007 08:54 AM
Dude, just make sure he knows to blast the primer sequences agains the genome first if he's trying to clone from gemoic DNA!
From the voice of experience ...
Posted by: Joolya | March 20, 2007 06:28 AM