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

Voronto

:: 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

FANSe

:: 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

MapSplice 2.1.8 – Mapping of RNA-seq reads for Splice Junction Discovery

MapSplice 2.1.8

:: DESCRIPTION

MapSplice is an algorithm for mapping RNA-seq data to reference genome for splice junction discovery.  MapSplice algorithm to detect splice junctions without any dependence on splice site features. This enables MapSplice to discover non-canonical junctions and other novel splicing events, in additional to the more common canonical junctions.

::DEVELOPER

Bioinformatics Lab @CS.UKy.edu

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 MapSplice

:: MORE INFORMATION

Citation

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery.
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J.
Nucleic Acids Res, 38(18):e178, 2010.

CompMap – Compressive Short Read Mapping

CompMap

:: DESCRIPTION

CompMap is a reference-based compression program to speed up read mapping to related reference sequences. CompMap is designed to eliminate repeat subsequences based on reference-base compression in the input curating database, which could contain complete genomes, plasmids, and/or other sequences.

::DEVELOPER

Zexuan ZHU

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

  CompMap

:: MORE INFORMATION

Citation:

CompMap: a reference-based compression program to speed up read mapping to related reference sequences.
Zhu Z, Li L, Zhang Y, Yang Y, Yang X.
Bioinformatics. 2014 Oct 4. pii: btu656

BAIT 1.4 – Organizing Genomes and Mapping Rearrangements in Single Cells

BAIT 1.4

:: DESCRIPTION

BAIT (Bioinformatic Analysis of Inherited Templates) is a software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

::DEVELOPER

Terry Fox Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • SAMtools
  • BEDtools
  • R
  • DNAcopy R package
  • gplots R package.

:: DOWNLOAD

 BAIT

:: MORE INFORMATION

Citation

Genome Med. 2013 Sep 13;5(9):82.
BAIT: Organizing genomes and mapping rearrangements in single cells.
Hills M1, O’Neill K, Falconer E, Brinkman R, Lansdorp PM.