SENCEL PARALIGN
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.
Advantages
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.
Databases
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
|
Nucleotide
|
Nucleotide
|
Nucleotide
|
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.
|