Please recommend short courses or self-study books for commonly used DNA softwar - (Oct/31/2006 )

Hi,

I'd appreciate if anyone can give me some recommendations. I've leanrt some basic usages of Blastn and all in some classes I took but the teacher didn't really get into much details of any of the softwares. Everything I leart were based on the "default" settings, and I have no clue on how to adjust any settings to my need or what they will do to my search. Also, I have always wanted to learn a software which I can use to design "universal primers" from common regions of a gene that has variations from different strains. I've tried to download and use MACAW for such purpose but found it difficult to use only becasue I have no clue how to adjust settings. Can anyone give me directions of how to approach this learning process so I can start to actually know how to use these softwares? Maybe some training lessions offered by public/private sectors or some good books. Thanks.

as far as blastn, I can only recommend what my old biochem teacher told me...take a sequence that you know, paste it in, and play with the settings to see what sort of differences you get. this is the best way, as opposed to memorization of different settings for different purposes