[Noob Q] I need a hand on sequence alignment

[bbs_r]

Hi, guys. I just got some trouble with sequence aligment...

If I would like to align my sequence with the mouse genome, which alignment tool would you prefer?

Also, if I would line up my primer with the mouse genome, which alignment tool do you use?

(if case if the tool is not within NCBI, please provide a link. Thank you)

Thank you very much for your help!

[Trev]

If you will work with your final alignment in future and you will use different programs, I wish advise ClustalW (ftp://ftp.ebi.ac.uk/pub/software/) program (it`s free).
But if you wants more friendly interface and funtionality, you should use Vector NTI (invitrogen.com) program. 10th version is free, as I know.
As for me, I usually use Vector and I dislike ClustalW, but sometimes I must use it.

[Trev]

I don`t understand your term "line up". In Russain we have several different meanings.

If "line up" = design
I prefer use for primer construction "Primer Premier" (but it is not free program). Aslo you can use Vector NTI. Primer Premier - more understandable.

[bbs_r]

I don`t understand your term "line up". In Russain we have several different meanings.

My original meaning of "line up" is: to put two sequences together and compare the difference between them.

[Trev]

My original meaning of "line up" is: to put two sequences together and compare the difference between them.

ok))

You may use Vector NTI and ClustalW. Links to this programs you can find in my first post of this topic.

[bbs_r]

Thanks mate, are there any difference between the online version of ClusterW (http://www.ebi.ac.uk/clustalw/) and the program version of ClusterW (ftp://ftp.ebi.ac.uk/pub/software/)?

[Trev]

there are no serious differences