[Noob Q] I need a hand on sequence alignment

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bbs_r
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[Noob Q] I need a hand on sequence alignment

Post by bbs_r » Tue Apr 04, 2006 7:39 am

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
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Post by Trev » Tue Apr 04, 2006 4:39 pm

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.
Last edited by Trev on Tue Apr 04, 2006 5:03 pm, edited 3 times in total.
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Post by Trev » Tue Apr 04, 2006 4:50 pm

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.
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Post by bbs_r » Thu Apr 06, 2006 9:51 am

Trev wrote: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. :lol:

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Post by Trev » Thu Apr 06, 2006 11:25 am

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

:) ok))

You may use Vector NTI and ClustalW. Links to this programs you can find in my first post of this topic.
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Post by bbs_r » Thu Apr 06, 2006 11:52 am

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/)?

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Post by Trev » Thu Apr 06, 2006 3:28 pm

there are no serious differences
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