KLab Software

 

KLab PCR: A tool that implements two algorithms to quantify the starting template in a PCR reaction. The first is a modified Ct strategy that assumes an ideal efficiency and is calculated for reference. The second employs a parametric fitting approach to construct a non-linear approximation to the reaction efficiency that is regressed backwards to establish a peak efficiency. The implementation can use data from a single PCR reaction, or from several reactions where the same primers are used yielding a consensus of peak efficiency. Reference: Platts AE, Johnson GD, Linnemann AK, Krawetz SA.; Real-time PCR quantification using a variable reaction efficiency model. Anal Biochem. 2008 Sep 15;380(2);315-22. Epub 2008 Jun5. Software downloadable

Knet: This utility finds pairs of genes with similar behavior across a gene expression dataset. It is intended to be used as a comparative tool to compare the network size (number of output rows) between N datasets with the same numbers of biological samples (input columns) and measured genes (input rows). Reference: Platts, A.E., Lalancette, C., Emery, B.R., Carrell, D.T. and Krawetz, S.A. (2010) Disease Progression And Solid Tumor Survival: A Transcriptome Decoherence Model. Molecular and Cellular Probes. 24:53-60. PMID: 19835949 Software downloadable

K-spmm: K-SPMM: a database of murine Spermatogenic Promoters Modules and Motifs. A web-based resource for the comparative analysis of promoter regions and their constituent elements in developing male germ cells. The system contains data on promoter regions in Sertoli cells, spermatogonia, spermatocytes and spermatids. TF Binding sites can be identified through their similarities to PWMs hosted in both JASPAR and TRANSFAC. Reference: Lu Y., Platts A. E., Ostermeier G. C., Krawetz S. A. K-SPMM: a database of murine spermatogenic promoters modules & motifs. BMC Bioinformatics 2006a; 7: 238.

LaraLink: Identify associations between certain tissues and diseases. Reference: Platts A. E., Moldenhauer J. S., Fayz B., Wang D., Borgaonkar D. S., Krawetz S. A. LARaLink 2.0: A comprehensive aid to basic and clinical cytogenetic research. Genet Test 2005; 9: 334-341.

Oligonucleotide Search: web-based tool for evaluating the propensity of primers to hybridize to similar sequences throughout the genome. Reference: Syst Biol Reprod Med. 2008 Mar-Apr;54(2):97-108. The KLAB Toolbox: a suite of in-house software applications for epigenetic analysis. Naismith L, Lalancette C, Platts AE, Krawetz SA. Software downloadable

Suite16: co-localizes and displays genomic features. Reference: Linnemann A. K., Platts A. E., Doggett N., Gluch A., Bode J., Krawetz S. A. Genomewide identification of nuclear matrix attachment regions: an analysis of methods. Biochem Soc Trans 2007; 35(Pt 3)612-617. Software downloadable

Synteny: Tool to investigate sequence conservation between species. Reference: Martins R. P., Krawetz S. A. Nuclear organization of the protamine locus. Reproduction in Domestic Ruminants, VI, J. L. Juengel, J. F. Murray, M. F. Smith. Nottingham University Press, NottinghamUK 2007b; 1-12. Software downloadable

Array Design: The efficacy of the KLab interspecies tiling program was demonstrated by interrogating the endogenous and human protamine loci in a transgenic mouse line (1). Species specific probe sets were designed by adapting a previously reported maskless array synthesis strategy (2). Reference: (1) Johnson G.D., P. A. E., Lalancette C., Goodrich R., Krawetz S.A. (In Press) Systems Biology in Reproductive Medicine. (2) Graf, S., Nielsen, F. G., Kurtz, S., Huynen, M. A., Birney, E., Stunnenberg, H., and Flicek, P. (2007; open soucre code is available at http://www.ebi.ac.uk/) Bioinformatics 23, i195-204. Software downloadable

Contact Details: For more information, suggestions, requests, or simply to say hi, please send email to steve@compbio.med.wayne.edu.