Introduction

Comparative genomics heavily relies on alignments of large and often complex DNA sequences. From an engineering perspective, the problem here is to provide maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accommodate the billions of base pairs of vertebrate genomes).Satsuma addresses all three issues through novel strategies: (i) cross-correlation, implemented via fast Fourier transform; (ii) a match scoring scheme that eliminates almost all false hits; and (iii) an asynchronous 'battleship'-like search that allows for aligning two entire fish genomes (470 and 217 Mb) in 120 CPU hours using 15 processors on a single machine.Satsuma is part of the Spines software package, implemented in C++ on Linux. The latest version of Spines can be freely downloaded under the LGPL license from http://www.broadinstitute.org/science/programs/genome-biology/spines/.

Publications

  1. Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
    Cite this
    Grabherr MG, Russell P, Meyer M, Mauceli E, Alföldi J, Di Palma F, Lindblad-Toh K, 2010-05-01 - Bioinformatics (Oxford, England)

Credits

  1. Manfred G Grabherr
    Developer

    -, Broad Institute of MIT and Harvard, United States of America

  2. Pamela Russell
    Developer

  3. Miriah Meyer
    Developer

  4. Evan Mauceli
    Developer

  5. Jessica Alföldi
    Developer

  6. Federica di Palma
    Developer

  7. Kerstin Lindblad-Toh
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT003426
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByKerstin Lindblad-Toh