[Biococoa-dev] whatsuuup?

[Koen van der Drift]

On Oct 3, 2005, at 11:40 PM, Charles Parnot wrote:

>
> I suppose there would be some positional information, where the  
> sequence are aligned in some specific ways, so an array of  
> sequences + an array of offset should do. The best way to start is  
> to agree on a good, simple but complete and consistent header and  
> then the implementation almost does not matter and can always be  
> modified in the future.
>

I am trying to figure out what you mean by the array of offset. I  
like to visualize things, so assume we have the following sequences  
that are related:

1. CCGTGGGTCCAGGATGA

2. ----GGGCCAGG----

3. --GTGGGGCCAGGATGA


Then the offset array would be like:

0, 4, 2


But it could also be:

-4, 0, -2


Am I on the right track here?


- Koen.