Demo search


SENCEL PARALIGN is a sequence database search application based on local sequence alignments. It incorporates the most sensitive algorithms for searching sequence databases based on local sequence alignments. Implementation of these algorithms at a very high speed has been achieved by exploiting the advanced parallel processing technology embedded in modern microprocessors.

The PARALIGN product sheet (PDF) gives an overview of important features.

Free online demo searches are available.

Free one month evaluation licenses are available for running the software on your own computer. Free licenses are also available for academic, non-profit usage.


The primary advantages of SENCEL PARALIGN are:

Higher quality results: Better sensitivity and selectivity than the common heuristic homology search programs. Allows you to get much better results. Click here for more information about the sensitivity and selectivity of the software.
Increased speed: You can get results faster, allowing you to perform more searches in larger databases. Click here for more information about the speed of the software.

Other advantages:

No proprietary hardware: This is a software-only solution, requiring no special purpose hardware.
Affordable: You can achieve better search speed and quality as with other solutions but using less expensive hardware. Sencel's software works on the most cost-effective commonly available hardware.
A solution for the future: The speed of the software improves as better hardware becomes available and it scales nearly linearly with the clock frequency of the microprocessors.
Flexible: The software scales well all the way from simple PCs to multi-processor servers and clusters. Just choose the power you need.

Search algorithms

SENCEL PARALIGN incorporate two high quality sequence homology database search algorithms with scientifically documented performance [1-4]. When you run the software you can choose which algorithm to use just by changing an option on the command line.

Smith-Waterman: The first algorithm is known as the Smith-Waterman algorithm [1,2], a rigorous, mathematically optimal algorithm. It is the gold standard for pairwise local sequence alignments. Sencel's patent-pending implementation of this algorithm [3] gives results identical to other implementations, but it is much faster.

ParAlign: The second algorithm is called ParAlign [4] and is a heuristic search algorithm. It gives results that are almost as good as the Smith-Waterman algorithm, but much faster. ParAlign is considerably more sensitive than all other heuristic algorithms, and it produces results indistinguishable from those of the Smith-Waterman algorithm. The patent-pending ParAlign algorithm has been shown to be as sensitive as the Smith-Waterman algorithm for detecting structural homologs of protein domains.

Click here for more information about the sensitivity and selectivity of the software.

Click here for more information about the speed of the software.


PARALIGN uses databases formatted by the NCBI formatdb tool, and can use most of the same databases as BLAST. See the user's guide for details.

Search modes

SENCEL PARALIGN can perform searches using both amino acid and nucleotide sequences. Five different modes of searches are possible as indicated in the table below.

Query sequence type
Database sequence type
Comparison type
Amino acid
Amino acid
Amino acid
Amino acid
Nucleotide (translated)
Amino acid
Nucleotide (translated)
Amino acid
Amino acid
Nucleotide (translated)
Nucleotide (translated)
Amino acid

System requirements

Click here for more information about system requirements for Sencel's software.