TAG 0.91 – Transcript Assembly by Mapping Reads to Graphs

TAG 0.91

:: DESCRIPTION

TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TAG

:: MORE INFORMATION

Citation:

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis.
Ye Y, Tang H.
Bioinformatics. 2015 Aug 29. pii: btv510.

TagMix – Genome-wide Tag SNPs Selection

TagMix

:: DESCRIPTION

TagMix is an integrated cross-populations LD-based, haplotype-based and principal component analysis genome-wide tag SNPs selection algorithm to efficiently identify informative variants, prioritized across multi-populations of low LD and high diversity populations for custom chip array.

::DEVELOPER

Emile CHIMUSA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TagMix

:: MORE INFORMATION

TCC 1.10.0 – Differential Expression Analysis for Tag Count data with Robust Normalization Strategies

TCC 1.10.0

:: DESCRIPTION

TCC provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES).

::DEVELOPER

Jianqiang Sun <wukong at bi.a.u-tokyo.ac.jp>, Tomoaki Nishiyama <tomoakin at staff.kanazawa-u.ac.jp>, Koji Kadota

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 TCC

:: MORE INFORMATION

Citation

TCC: an R package for comparing tag count data with robust normalization strategies.
Sun J, Nishiyama T, Shimizu K, Kadota K.
BMC Bioinformatics. 2013 Jul 9;14:219. doi: 10.1186/1471-2105-14-219.

PDBpaint 20111209 – Tag Protein Structures with Sequence Annotations

PDBpaint 20111209

:: DESCRIPTION

PDBpaint is a simple tool that displays protein sequence features gathered from bioinformatics resources on top of protein structures, which are displayed in an interactive window (using the Jmol Java viewer). PDBpaint can be used either with existing protein structures or with novel structures provided by the user.

::DEVELOPER

Computational Biology and Data Mining Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PDBpaint

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 15;27(18):2605-6. Epub 2011 Jul 14.
PDBpaint, a visualization webservice to tag protein structures with sequence annotations.
Fournier D, Andrade-Navarro MA.

FSTVAL – Flanking Sequence Tag Validator

FSTVAL

:: DESCRIPTION

FSTVAL is an open access web tool to manage bulk flanking sequence tags (FSTs).FSTVAL automatically evaluates the FSTs and finds the best mapping positions of the FST against a known genome sequence.

::DEVELOPER

FSTVAL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FSTVAL

:: MORE INFORMATION

Citation

Plant Methods. 2012 Jun 18;8(1):19. doi: 10.1186/1746-4811-8-19.
FSTVAL: a new web tool to validate bulk flanking sequence tags.
Kim JS1, Kim J, Lee TH, Jun KM, Kim TH, Kim YH, Park HM, Jeon JS, An G, Yoon UH, Nahm BH, Kim YK.

TagGD – DNA Tag Generation and Demultiplexing

TagGD

:: DESCRIPTION

TagGD (DNA-based Tag Generator and Demultiplexor), a fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy.

::DEVELOPER

Pelin Akan (Phone: 0852481452)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows

:: DOWNLOAD

  TagGD

:: MORE INFORMATION

Citation

PLoS One. 2013;8(3):e57521. doi: 10.1371/journal.pone.0057521. Epub 2013 Mar 4.
TagGD: fast and accurate software for DNA Tag generation and demultiplexing.
Costea PI, Lundeberg J, Akan P.

tagIMPUTE 1.0 – Tag-based imputation

tagIMPUTE 1.0

:: DESCRIPTION

tagIMPUTE (Tag-based imputation) is a command-line program for the imputation of untyped SNPs. tagIMPUTE is based on a few flanking SNPs that can optimally predict the SNP under imputation.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 tagIMPUTE

:: MORE INFORMATION

Citation

Hu, Y. J. and Lin, D. Y. (2010),
Analysis of Untyped SNPs: Maximum Likelihood and Imputation Methods“,
Genet Epidemiol. 2010 Dec;34(8):803-15.

F-Seq 1.84 – Feature Density Estimator for High-Throughput Sequence Tags

F-Seq 1.84

:: DESCRIPTION

F-Seq is a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

::DEVELOPER

Furey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

 F-Seq

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Nov 1;24(21):2537-8. doi: 10.1093/bioinformatics/btn480. Epub 2008 Sep 10.
F-Seq: a feature density estimator for high-throughput sequence tags.
Boyle AP, Guinney J, Crawford GE, Furey TS.

FastTagger 1.0 – Genome-Wide Tag SNP selection

FastTagger 1.0

:: DESCRIPTION

FastTagger is a software to calculate multi-marker tagging rules and select tag SNPs based on multi-marker LD. FastTagger uses several techniques to reduce running time and memory consumption.

::DEVELOPER

Limsoon Wong Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux/ Windows
  • C++ Compiler

:: DOWNLOAD

 FastTagger

:: MORE INFORMATION

Citation:

Guimei Liu, Yue Wang, Limsoon Wong.
FastTagger: An Efficient Algorithm for Genome-Wide Tag SNP selection using multi-marker linkage disequilibrium
BMC Bioinformatics, 11:66, February 2010.

SAGExplore – Map SAGE tags against Genomic Annotation

SAGExplore

:: DESCRIPTION

SAGExplore is a server for the mapping of SAGE tags against a genomic annotation.

::DEVELOPER

Francisco Melo Ledermann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W163-8. Epub 2007 Jul 10.
SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation.
Norambuena T, Malig R, Melo F.