Hi all,

In the SOLiD system, read are mapped a color-space encoded version of  
the reference sequence in question, after which start and end  
coordinates are reported. Base-space sequence can then (if needed) be  
extracted from the reference sequence using the given coordinates.

There is a "double encoding"-system, where the colors (0, 1, 2, 3) are  
changed to letters (A, C, G, T) to trick certain software to work with  
SOLiD data. This does not correspond to the actual base-space  
sequence, it's only a representation of the color-space sequence. I  
guess it would be possible to use this trick to make BioStrings and  
ShortRead work with SOLiD data.

However, one very important feature of the SOLiD system, is that the  
reverse complement sequence corresponds to the reverse color-space  
sequence (there is no "complement" in color-space). This means that  
the algorithm for returning the rev-comp sequence when prior to  
matching on the (-)-strand need to be re-written to report the reverse  
sequence instead of the rev-comp.

Did all this make sense...? Basically, I think it would be possible to  
make it work if the colors are "double-encoded" and the internal  
function that rev-comps a sequence is modified to report the reverse.

Best
Daniel Klevebring


On 5 feb 2009, at 01.39, Martin Morgan wrote:

> , once reads are represented
> as traditional nucleotide sequences (which I guess they must be at
> some point?).

--

Contact information:

Daniel Klevebring
M. Sc. Eng., Ph.D. Student
Dept of Gene Technology
Royal Institute of Technology, KTH
SE-106 91 Stockholm, Sweden

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