:: DESCRIPTION
In NeoCodon, you have less than 2 minutes to match 8 DNA codons with their RNA counterparts. You can count on enzymes to help you achieve this crucial task. But beware, viruses are trying to mess up with your work…
::DEVELOPER
Adrien Contesse (kloxpou@gmail.com)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
DNA/RNA/Protein and General Molecular Weight Calculator designed by the editors of Current Protocols. Type in or copy/paste any nucleic acid base sequence, any protein or peptide amino acid sequence (in one- or three-letter codes accessible from a convenient menu), or any standard chemical formula, and obtain the molecular weight. Allows estimates of the molecular weights of unknown nucleic acid or protein/peptide sequences on the basis of sequence length and average base/amino acid molecular weights. Also includes a list of 1200 of the most commonly encountered organic and inorganic compounds, which may be immediately selected in order to calculate their molecular weights, as well as an easy-to-access list of the chemical elements, which may be plugged into any chemical formula.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
DNA/RNA/Protein and General Molecular Weight Calculator
:: MORE INFORMATION
:: DESCRIPTION
BASTA contains an implementation of a Bayesian model-based method for unsupervised classification of tissue samples based on DNA copy number amplifications.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Marttinen, Pekka, Myllykangas, Samuel and Corander, Jukka (2009)
Bayesian clustering and feature selection for cancer tissue samples
BMC Bioinformatics 2009, 10:90
:: DESCRIPTION
nxCode is a tool for designing and decoding DNA barcodes for multiplexing on high throughput sequencing platforms.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MPCBS (Multi-Platform Circular Binary Segmentation) is a software which pools statistical evidence across platforms during segmentation, and does not require pre-standardization of different data sources. It involves a weighted sum of t-statistics, which arises naturally from the generalized log-likelihood ratio of a multi-platform model.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhang, NR, Senbabaoglu, Y and Li, J, 2010,
Joint Estimation of DNA Copy Number from Multiple Platforms.
Bioinformatics, 26, 153-160.
:: DESCRIPTION
SEWAL (Sequence Evolution With Adaptive Landscapes) is an open source tools for next generation DNA sequencing analysis and visualization. SEWAL provides a new platform for DNA sequence analysis and visualization of large data sets generated by massive sequencing to perform functional in vitro genetics. The visualization incorporates the underlying LSH information in a visually intuitive manner to generate mutant spectra. When the differences in these plots resulting from altered selective pressures are visualized, they can represent projections of the hyperdimensional fitness landscape, if the frequency of the sequences has been demonstrated to correlate with phenotypic fitness
::DEVELOPER
Pitt (jpitt@fhcrc.org), Rajapakse, and Ferre-D’Amare HHMI FHCRC
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2010 Dec;38(22):7908-15. Epub 2010 Aug 6.
SEWAL: an open-source platform for next-generation sequence analysis and visualization.
Pitt JN, Rajapakse I, Ferré-D’Amaré AR.
:: DESCRIPTION
GS De Novo Assembler (Newbler) is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Science, a Roche diagnostic.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PatScan (scan_for_matches) is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input.
::DEVELOPER
Ross Overbeek (overbeek@mcs.anl.gov); David Joerg and Morgan Price
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
RepeatScout is a tool to discover repetitive substrings in DNA.
::DEVELOPER
Alkes L. Price, Neil C. Jones and Pavel A. Pevzner
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
De novo identification of repeat families in large genomes.
Price AL, Jones NC, Pevzner PA.
Bioinformatics. 2005 Jun;21 Suppl 1:i351-8.
:: DESCRIPTION
SIMULATOR is a software to simulate DNA and protein datasets with well-defined insertion-deletion dynamics according to a user-given tree.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Roland Fleißner (2004) Sequence alignment and phylogenetic inference. Logos Verlag, Berlin.