:: DESCRIPTION
McQSAR generates quantitative structure-activity relationships (QSARs) using the genetic function approximation paradigm.
::DEVELOPER
Structural Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Mikko J. Vainio and Mark S. Johnson (2005)
McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms.
J. Chem. Inf. Model. 45, 1953-1961.
:: DESCRIPTION
SimPed is a program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies.
::DEVELOPER
Human Genome Sequencing Center
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Leal, Yan, Muller-Myhsok (2005),
“SimPed: a simulation program to generate haplotype and genotype data for pedigree structures“,
Human Heredity, 60(2):119-122.
:: DESCRIPTION
Mutagenesis Primer Generator is a simple windows GUI program to generate mutagenesis primer by inputting sequence, amino acid number, and letter of amino acid you want to mutate to.
::DEVELOPER
Jonas Lee (jonaslee@berkeley.edu) in Prof. S H Kim’s Lab UC Berkeley
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
gs can be used to generate samples in testing algorithms for tag SNP selection, haplotype inference, as well as epistatic detection.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Li, J and Y Chen.
Generating samples for association studies based on HapMap data.
BMC Bioinformatics 9:44, 2008.
:: DESCRIPTION
HangOut is a software for a single domain with specified insertion position, cleans erroneously extended PSI-BLAST alignments to generate better profiles.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
B.H. Kim, Q. Cong, N.V. Grishin (2010)
“HangOut: generating clean PSI-BLAST profiles for domains containing long insertions“.
Bioinformatics (2010) 26 (12): 1564-1565.
:: DESCRIPTION
CoverageTool implements the algorithm presented in Archer et al., 2011 (Submitted). The constructs generated by the algorithm can be used as a metric in order to characterize the k-mer coverage accross an alignment.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Archer, J., Williams, S.G., et al. The characterization of HIV-1 k-mer space – a prerequisite to vaccine design. Submitted.
:: DESCRIPTION
Time-warp is the global alignment program; several alternative methods are available to generate a similarity matrix; a dynamic programming algorithm finds the optimal alignment path through the matrix. As well as the Gene-warp (see above), Time-warp takes as an input two time-series microarray datasets, containing orthologous expression profiles in the corresponding rows of the two matrices.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.
:: DESCRIPTION
Gene-warp is a tool to select ortholog pairs with best alignments and to explore alignment paths (not expression profiles!) shared by many genes. The program takes as an input two related datasets, containing profiles of orthologous genes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.
:: DESCRIPTION
LOLA (LOgos Look Amazing) is a tool for generating sequence logos using Position Weight Matrix based protein profiles. LOLA allows you to generate custom sequence logos by setting parameters such as logo height, trim percentage, and residue colour scheme. You can also generate “logo trees” based on clustered protein profiles to analyze binding motif classes. Sequence logos and logo trees can be saved in various formats including PDF, PNG, and JPEG.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Tonikian, R. et al.(2008)
A Specificity Map for the PDZ Domain Family.
PLOS Biology, 6, 9: 2043-2059.
