[Bioperl-l] Re:Smith waterman Alignment

[Ewan Birney]

On 12 Jun 2003, M K. Govind wrote:

> Hi all,
>
> I am trying to align 2 sequences using the smithwaterman alignment
> and i get the following error. Could you please elaborate more on
> this.


This is a deep error inside the divide and conquor routine here, and ...
hmmm... are you using

  (a) very, very long sequences?

  (b) weird sequences with letters not in the matrix

I haven't seen this sort of thing for a while.



>
> ****************************************************************
> Warning Error
>          In full dc program, passed bad indices, indices passed
> were -1:-1[-1]
> to 1324:961[1]
>
> Warning Error
>          In recaluclating PackAln with state INSERT, from
> [476,959,3], got a
> bad source state. Error!
> Warning Error
>          Between state [848,3,3] and [1324,962,1] got no labels...
> labelling
> as UNKNOWN
> Warning Error
>          In full dc program, passed bad indices, indices passed
> were -1:-1[-1]
> to 1324:961[1]
>
> Warning Error
>          In recaluclating PackAln with state INSERT, from
> [476,959,3], got a
> bad source state. Error!
> Warning Error
>          Between state [848,3,3] and [1324,962,1] got no labels...
> labelling
> as UNKNOWN
>
> **********************************************************************
>
> Thanks in advance
>
> -Govind
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