BFAST using GPUs

[Sukesh]

Can anyone explain me "What is CAL" in BFAST?

I understood First part i.e Indexing In BFAST...and also Second part i.e Smith waterman Part..But I am Unable to get CAL....which i believe is input to Smith Waterman Part...


So can anyone explain How do we get CAL from indexing and use it in Smith Waterman Code...

I have refereed PLOS one Paper "BFAST - An Alignment tool "..But no success ..


help!!!!

[nilshomer]

A CAL is an acronym for a "Candidate Alignment Location". Using the seed and extend method, a short list of possible alignment locations (CALs) is created, then the Smith Waterman algorithm is used to examine each CAL to find the best mapping.

[Sukesh]

Hello Sir,

Can you explain Me CAL with an Example...or any Links where i can Understand it more efficiently.

For Example : if my reference string is "aaaaaagtcggttagtccagtttttttttttttggggggagtgggccccctagtccccagt"

Query String is : agt

So what should be my CAL? after Indexing ...

[nilshomer]

What the set of CALs will be depends on what is your indexing strategy. You sound like you have a very basic understanding of mapping/alignment, so please check out the relevant literature to get up to speed. For example, the following paper is a good introduction and also references a lot very useful papers: http://dx.doi.org/10.1093/bib/bbq015.