Tag: Matching

PriSM – Primer Selection and Matching for Amplification of Viral Genomes

PriSM

:: DESCRIPTION

PriSM is a set of algorithms designed specifically to create degenerate primers for the amplification and sequencing of short viral genomes while maintaining sample population diversity.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Yu Q, Ryan EM, Allen TM, Birren BW, Henn MR, Lennon NJ (2011)
PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.
Bioinformatics 27(2): 266-267.

sigMatch – Fast and Scalable Multi-Pattern Matching

sigMatch

:: DESCRIPTION

sigMatch is a fast, versatile,and scalable technique for multi-pattern signature matching. At its heart, sigMatch organizes the signature database into a (processor) cache-efficient q-gram index structure, called the sigTree.The sigTree groups patterns based on common sub-patterns, suchthat signatures that don’t match can be quickly eliminated from the matching process. The sigTree also uses parallel Bloom filters and a technique to reduce imbalances across groups, for improved performance. Using extensive empirical evaluation across three diverse domains, we show that sigMatch often outperforms existing methods by an order of magnitude or more.

::DEVELOPER

Jignesh M. Patel 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 sigMatch

:: MORE INFORMATION

Citation:

SigMatch: Fast and Scalable Multi-Pattern Matching,
R. Kandhan, N. Teletia and J. M. Patel,
VLDB 2010.