GoRAMPAGE – Workflow for Promoter Detection by 5′-read Mapping

GoRAMPAGE

:: DESCRIPTION

GoRAMPAGE is a workflow for promoter detection by 5′-read mapping.

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GoRAMPAGE

:: MORE INFORMATION

Citation

Raborn RT, Brendel VP.
Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes.
Methods Mol Biol. 2019;1858:99-116. doi: 10.1007/978-1-4939-8775-7_9. PMID: 30414114.

BPrimm 1.12 – Bayesian and Penalized Regression in Multiple Loci Mapping

BPrimm 1.12

:: DESCRIPTION

BPrimm (Bayesian and Penalized regression in multiple loci mapping) includes a set of tools for simultaneously multiple loci mapping, and two novel methods named the Bayesian adaptive Lasso and the Iterative Adaptive Lasso

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 BPrimm

:: MORE INFORMATION

Citation

Wei Sun, Joseph G. Ibrahim and Fei Zou
Genome-wide Multiple Loci Mapping in Experimental Crosses by the Iterative Adaptive Penalized Regression
Genetics May 2010 vol. 185 no. 1 349-359

SQTL – Semiparametric QTL Mapping in General Pedigrees

SQTL

:: DESCRIPTION

SQTL is a semiparametric quantitative trait loci mapping method to human gene expression data. The SQTL mapping method is rank-based and therefore robust to non-normality and outliers.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 SQTL

:: MORE INFORMATION

Citation

BMC Proc. 2007;1 Suppl 1:S83. Epub 2007 Dec 18.
Semiparametric methods for genome-wide linkage analysis of human gene expression data.
Diao G, Lin DY.

CrossClassify – Mapping between different Taxonomic Classifications

CrossClassify

:: DESCRIPTION

CrossClassify is a tool for mapping different metagenomic analyses on a common taxonomic classification

::DEVELOPER

the Algorithms in Bioinformatics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

CrossClassify

:: MORE INFORMATION

Citation

Balvočiūtė M, Huson DH.
SILVA, RDP, Greengenes, NCBI and OTT – how do these taxonomies compare?
BMC Genomics. 2017 Mar 14;18(Suppl 2):114. doi: 10.1186/s12864-017-3501-4. PMID: 28361695; PMCID: PMC5374703.

GGD-Lasso – Graph-regularized dual Lasso for robust eQTL mapping

GGD-Lasso

:: DESCRIPTION

GGD-Lasso (Graph-regularized Dual Lasso) is a robust approach for eQTL mapping.

::DEVELOPER

Wei Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler / MatLab

:: DOWNLOAD

 GGD-Lasso

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i139-i148. doi: 10.1093/bioinformatics/btu293.
Graph-regularized dual Lasso for robust eQTL mapping.
Cheng W, Zhang X, Guo Z, Shi Y, Wang W.

Voronto – Mapping Gene Expression to Ontologies with Voronoi Tessellations

Voronto

:: DESCRIPTION

Voronto is a tool that integrates expression data and biological ontologies, allowing the analyst to explore the whole ontology and detect changes on expression patterns inside the ontology.

::DEVELOPER

RODRIGO SANTAMARÍA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/MacOS
  • Java

:: DOWNLOAD

 Voronto

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2281-2. doi: 10.1093/bioinformatics/bts428. Epub 2012 Jul 4.
Voronto: mapper for expression data to ontologies.
Santamaría R1, Pierre P.

SIfTER 2015 – Mapping Protein Conformation Spaces

SIfTER 2015

:: DESCRIPTION

SIfTER is a structure-guided memetic, cellular, and multiscale evolutionary algorithm for mapping protein conformation spaces. It is based instead on stochastic optimization to circumvent the computational challenge of exploring the breadth of a protein’s structure space.

::DEVELOPER

Computational Biology lab, George Mason University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SIfTER

:: MORE INFORMATION

Citation

Clausen R, Ma B, Nussinov R, Shehu A.
Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm.
PLoS Comput Biol. 2015 Sep 1;11(9):e1004470. doi: 10.1371/journal.pcbi.1004470. PMID: 26325505; PMCID: PMC4556523.

TTS mapping – Triplex Target DNA Site Mapping

TTS mapping

:: DESCRIPTION

TTS mapping is a web-based search engine to find and annotate pTTSs within human genome region of interest. The engine provides descriptive statistics of pTTSs in a given region and its sequence context. Different annotation tracks of TTS-overlapping gene region(s), G-quadruplex motifs, CpG Island, miRNA precursors, miRNA targets, transcription factor binding sites (TFBSs), Single Nucleotide Polymorphisms (SNPs), small nucleolar RNAs (snoRNA), and repeat elements are also mapped based on sequence location provided by UCSC genome browser, G-quadruplex database and several other datasets.

::DEVELOPER

the Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2009 Dec 3;10 Suppl 3:S9. doi: 10.1186/1471-2164-10-S3-S9.
TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome.
Jenjaroenpun P1, Kuznetsov VA.

TreqCG 0.3 – Clustering Accelerates High-Throughput Sequencing Read Mapping

TreqCG 0.3

:: DESCRIPTION

TreqCG is a method to accelerate and improve read mapping based on an initial clustering of up to billions of high-throughput sequencing reads yielding clusters of high stringency and a high degree of overlap.

::DEVELOPER

Schliep lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 TreqCG

:: MORE INFORMATION

Citation

Mahmud, Md and Schliep, Alexander.
TreQ-CG: Clustering Accelerates High-Throughput Sequencing Read Mapping (2014)

FANSe 2 – Fast and Accurate Mapping tool for Nucleotide Sequencing Datasets

FANSe 2

:: DESCRIPTION

FANSe2 is a mapping algorithm which can map a billion reads in hours with ultimate and robust accuracy.

::DEVELOPER

FANSe2 team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 FANSe

:: MORE INFORMATION

Citation

Zhang G *, Fedyunin I, Kirchner S, Xiao C, Valleriani A, Ignatova Z
FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads
Nucl. Acids Res. (2012) 40 (11): e83. doi: 10.1093/nar/gks196

FANSe2: A Robust and Cost-Efficient Alignment Tool for Quantitative Next-Generation Sequencing Applications.
Chuan-Le Xiao, Zhi-Biao Mai, Xin-Lei Lian, Jia-Yong Zhong, Jing-jie Jin, Qing-Yu He *, Gong Zhang *
PLoS One. 2014 Apr 17;9(4):e94250 DOI: 10.1371/journal.pone.0094250