DeCypher Smith-Waterman Solution

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bioinformatics and text mining solutions

Section Topics:

• Introduction
• NextEngine Accelerator
• Tera-BLAST
• Tera-Probe
• GeneDetective
• HMM Solution
• Smith-Waterman
• Algorithms
• Interfaces
• Configurations
• Published Citations

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DeCypherSW™ (Smith-Waterman and Framesearch)

High-sensitivity sequence analysis

Smith-Waterman is a well-established algorithm for local sequence alignment. Since 1981, it has been an essential tool for nucleic and protein comparisons due to its ability to guarantee optimal local alignments. But with today's genomic data output from next-generation sequencing platforms, Smith-Waterman software has been eclipsed by faster search tools such as BLAST (at the expense of sensitivity).

However TimeLogic's high performance Smith-Waterman is preferable to BLAST for many genomics search tasks, including:

Comparing evolutionarily divergent proteins
Mapping optimal microarray probes within a genome
Mapping oligos to a reference sequence with high sensitivity
All-to-all sequence comparisons within a clustering workflow
Small RNA studies

The Smith-Waterman implementation for the TimeLogic FPGA solutions accelerates dynamic programming calculations for research groups that demand high sensitivity and speed.

Smith-Waterman is included with the CodeQuest workstations and is an available module for the DeCypher Enterprise solutions, where it complements the other sequence comparison modules, including Tera-BLAST, HMM, and GeneDetective.

Interleaving alignments across reading fames

The Smith Waterman algorithm suite includes a comprehensive set of frameshift tolerant search tools. Framesearch helps you identify coding sequences in low quality DNA sequences—such as CE sequence reads, EST and BAC databases—where sequencing errors and indels introduce shifts in open reading frames. DeCypher’s powerful acceleration enables the use of these sensitive, dynamic methods without a large computing infrastructure. Symmetric Frame Independent (a symmetric version of Framesearch) extend frame-tolerance across multiple reading frames in the query and the target.

Smith-Waterman Search Methods

Algorithm	Query	Target	Description	Applications
Smith-Waterman	NT	NT	like BLASTN, more sensitive, allow gaps	Minimize cross-hybridization and maximize microarray specificity find and mask repetitive elements find regulatory regions "No compromise" homology modeling—find global alignments of your protein sequence to roteins for which structure is known
Smith-Waterman	AA	AA	similar to BLASTP but more sensitive, allows gaps
Double-Affine Smith-Waterman	NT	NT	SW, allow very long gaps	map cDNAs onto genomes, can gap over long introns
	AA	AA	SW, allow very long gaps	situations where entire domains are deleted between otherwise homologous proteins
	NT	AA	SW, allow very long gaps	map proteins onto genomes, can gap over long introns, if in frame
FrameSearch	NT	AA	like BLASTX, more sensitive, can align across gaps and frameshifts	assign tentative functions to EST Overcomes limitations in less sensitive gene finding programs
FrameSearch	AA	NT	like TBLASTN, more sensitive, can align across gaps and frameshifts
Symmetric Frame Independent™	NT	NT	Solves indel issues with EST and other low coverage nucleic data by conducting a sensitive protein domain search between your nucleic query and the nucleic database, with frame shifting as needed.	similar to TBLASTX, but more sensitive, allows for gaps and frameshifts

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