Sequence Alignment

Wunsch

I tryed to align two sequences
CCATTGGAGTA
and CATAGA
using Needleman-Wunsch algorithm but it only gives me 2 alignment resutls
CCATTGGAGTA
C-A-T--AG-A
and
CCATTGGAGTA
C-AT---AG-A

while I thought it should be 4 results because the first C in the second sequence is also permutable, right ?

So can you tell me how to take out the other two alignments ?

Thank you very much inadvance

iansmith

You should be able to change some parameter in the software option. You can change the gap penalty. Some alignment software also have problem when it comes to the first base pair permutation.

Wunsch

Thank iansmith, I solve that problem with a pen and a piece of paper only..
But i am still really wanting to know how a software parameter change would be able to handle that problem, what does such a software do to get 4 alignments ?
This is what I took from my biology class, talking with me about software thingies I think is like pouring water on a duck's head because I actually don't understand a thing at all.

Thank you so very much in advance and a "Happy New Year" from me to you too...

Wunsch

I never get any help from anyone except iansmith !!!!!

Jikx

During class, we were pointed to ClustalW (http://www.ebi.ac.uk/clustalw/) to do sequence alignments. Click the FAQ, and walla! It gives you help on exactly what all those insane options do...

And don't dispair, bioinformatics is a tough subject - and gets worse. Once I waltzed into my uni's computer labs to check my email and saw my friends (who were doing biomedical science) crying during their bioinformatics prac

iansmith

For 2 sequence aligment you can use Blast 2 sequence and you easily change so parameter.
http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi

For Clustal, I prefer to use the version available at the Biology Workbeanch of UCSD
http://workbench.sdsc.edu/

You need to register and it is free. Also you get a bunch of other bioinformatic tools.

I also took a grad level class. You need to understand the principle and theory behind bioinformatics. It make more sense once you understand the basics. My class was mostly about sequence alignment, BLAST and making threes.

Wunsch

Thank you jikx
iansmith, I know that was my mistake, I am really sorry. Can you tell me how to do now ??? I don't know what i should do. I am really stuck!
By the way, would you also tell me what lies behind bioinformatics ?

Jikx

Just paste this in the big white box (from the site i mentioned above):


>FOSB_Wunsch1 Protein fosA
CCATTGGAGTA

>FOSB_Wunsch2 Protein fosB
CATAGA


and you get an output like this:
http://www.ebi.ac.uk/cgi-bin/clustal...52860&poll=yes

which is an output before you muck around with all the settings like window length, gap extensions etc (the FAQ can help you there) .. however, these programs are more for sequences which are hundreds of of basepairs long!

iansmith

Wunsch, do you have any theoritical part for class.

If you don't:
First, you need to understand the mathematical models that are behind bioinformatics. You should look the Wright-Fisher model, Hardy-Weinberg Equilibrium, and Neutral model.
Second, you need to understand probability and how it applies to bioinformatics.
Third, try to understand what is behind the scoring methods such as the blossom scoring matrix.