:: 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
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
the Science for Life Laboratory, Uppsala University,
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
TCC provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
tagSNPfinder is a software of Cross entropy Monte Carlo methods for SNP selection. TagSNPFinder defined a novel multilocus LD measure ER with generalized mutual information. We also designed a general scheme to select ‘tagging’ SNPs through combining the association and diversity together. Currently TagSNPFinder have routines to select Tagging SNPs with exhaustive search forward, backward, and stepwise selection.
::DEVELOPER
Statistical Genetics and Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Liu, Z., Lin, S., Tan, M. (2006)
Genome-wide tagging SNPs with entropy-based Monte Carlo methods.
Journal of Computational Biology, 13, 1606-1614
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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 (CBDM) Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis.
Ye Y, Tang H.
Bioinformatics. 2015 Aug 29. pii: btv510.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
