SWAMP Align - Shannon Steinfadt

Welcome to SWAMP Align

You've made it to a portal for high performance parallel algorithms and adaptations for Smith-Waterman style sequence alignments. Thorough testing, fast speeds, and more information from your data. SWAMP Align.

What IS SWAMP?

box SWAMP is the acronym for Smith-Waterman using Associative Massive Parallelism. The Smith-Waterman algorithm is a well-known and used local sequence alignment algorithm for aligning two strings (sequences) of genomic data. The idea is to discover similar (homologous) regions between the two sequences. SWAMP is a suite of algorithms that extend, parallelize, and optimize the basic approach that Smith-Waterman utilizes. Check out the SWAMP Page for more information.

Ask about asc

box ASC is an associative computing model and the corresponding. The model is a single-instruction multiple data SIMD paradigm with several additional features designed to allow for fast, efficient searching based on content.

Updates

November 2009

If you are attending Supercomputing SC'09 conference, stop by to visit Shannon at the ACM Student Research Poster Competition. The poster is titled Large-Scale Wavefront Parallelization on Multiple Cores for Sequence Alignment. She is the recipient of the Broader Engagement Grant for SC for the second year.

September 2009

Invited speaker for the CRA-W Workshop at Grace Hopper Celebration of Women in Computing - The Road to Graduate School

Shannon started a Graduate Research Assistantship at Los Alamos National Lab with the Decision and Risk Anaylsis, continuing her research with parallel and HPC Smith-Waterman sequence alignment.

June 2009

Shannon held a summer position at Los Alamos National Laboratory with the Performance and Architectures Lab. She spent the summer looking at performance metric and parallel algorithms on several architectures, including SSE intrinsics and JumboMem.

Shannon Steinfadt and Kevin Schaffer had a paper that appeared in the 4th Ohio Collaborative Conference for Bioinformatics (OCCBIO), Cleveland, Ohio, June 15-17, 2009 “Parallel Approaches for SWAMP Sequence Alignment.”