Parametric k-best alignment

Details Parametric k-best alignment Parametric k-best alignment

2008-09-09

arxiv.org/abs/0809.1473v1

Biology

Quantitative Biology

Populations and Evolution

1 figure and 2 tables

Scientific paper

Optimal sequence alignments depend heavily on alignment scoring parameters. Given input sequences, {\em parametric alignment} is the well-studied problem that asks for all possible optimal alignment summaries as parameters vary, as well as the {\em optimality region} of alignment scoring parameters which yield each optimal alignment. But biologically correct alignments might be {\em suboptimal} for all parameter choices. Thus we extend parametric alignment to {\em parametric $k$-best alignment}, which asks for all possible $k$-tuples of $k$-best alignment summaries $(s_1, s_2, ..., s_k)$, as well as the {\em $k$-best optimality region} of scoring parameters which make $s_1, s_2, ..., s_k$ the top $k$ summaries. By exploiting the integer-structure of alignment summaries, we show that, astonishingly, the complexity of parametric $k$-best alignment is only polynomial in $k$. Thus parametric $k$-best alignment is tractable, and can be applied at the whole-genome scale like parametric alignment.

Affiliated with

Also associated with

No associations

Rating

Parametric k-best alignment does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Parametric k-best alignment, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Parametric k-best alignment will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-210288