SigMA – Signature Multivariate Analysis for low statistics SNV data

SigMA

:: DESCRIPTION

SigMA detects mutational signatures from the SNV calls of whole-genome, exome or targeted gene panel data.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

SigMA

:: MORE INFORMATION

Citation

Gulhan DC, Lee JJ, Melloni GEM, Cortés-Ciriano I, Park PJ.
Detecting the mutational signature of homologous recombination deficiency in clinical samples.
Nat Genet. 2019 May;51(5):912-919. doi: 10.1038/s41588-019-0390-2. Epub 2019 Apr 15. PMID: 30988514.

Sigma 2.0 BETA – Non-coding DNA Sequence Alignment

Sigma 2.0 BETA

:: DESCRIPTION

Sigma (Simple greedy multiple alignment) is an alignment program with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence.This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step.

::DEVELOPER

RAHUL SIDDHARTHAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Sigma

:: MORE INFORMATION

Citation:

Rahul Siddharthan,
“Sigma: multiple alignment of weakly-conserved non-coding DNA sequences“,
BMC Bioinformatics 7:143 (2006)

SIGMA 1.0.2 – Strain-level Identification of Genomes from Metagenomic Analysis for Biosurveillance

SIGMA 1.0.2

:: DESCRIPTION

SIGMA is a novel sequence similarity-based approach for strain-level identification of genomes from metagenomic analysis for biosurveillance.

::DEVELOPER

the Pan lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

SIGMA

:: MORE INFORMATION

Citation

Sigma: Strain-level Inference of Genomes from Metagenomic Analysis for Biosurveillance.
Ahn TH, Chai J, Pan C.
Bioinformatics. 2014 Sep 29. pii: btu641