MeltSim The DNA Melting Simulator
Download

MeltSim Ranking & Summary

MeltSim Tags

gene Genome home budget software windows 2007 fifa 98 jar file mobile backtrack 5 download data entry speed wav to text mytunes itunes 7.5 ygf ksea pleased eggsucker 2 serial google maps.sis embed .srt in

MeltSim Description

MeltSim is a statistical-mechanical program for calculating melting (denaturation) curves (derivative profiles) and maps of DNA, from genes to genomes. The model is the one-dimensional Ising lattice to which loop entropy has been appended. The original algorithm is that of Poland & Scheraga and Poland, with the Fixman & Friere approximation of the loop entropy by a sum of exponentials. Parameters in Poland's original algorithm were evaluated by Blake & Delcourt and provide near-quantitative agreement between observed and calculated Tm, amplitudes, breadths, and areas of transitions obtained under equilibrium conditions. The program stores the results of the operation in a log file that allows you to review important information and operations. Main features: The input (sequence) file requires no special format. Bases can be in uppercase and/or lowercase, and no line breaks are required. However, only the letters A, C, G, and T are counted as bases. With the helper application called COMPILE, specific sequence locations in GenBank-formatted files can be converted and read by MeltSim 1.0 for Windows. A title will be automatically added to the top of the graph if the first line of the input file contains text beginning with the pound sign (#). Bases are normally read in blocks of 100,000 bp and the d(theta)/dT (the first derivative of the portion unmelted, with temperature) vs. T values are averaged as more bases are read. The melting map file gives data for the very last block melted. MeltSim 1.0 for Windows can be directed to melt in blocks marked with an asterisk (*) in the input file. It can also read any part of a sequence by giving the start and stop locations. Multiple input files can be melted sequentially by using the asterisk wildcard (*) in the file name. With the automatic print function, MeltSim 1.0 for Windows can be left to work on any number of files, printing graphs as it goes. An output file is produced of melting curve coordinates (d/dT as a function of T). Another output file is produced of melting map coordinates (T and theta as functions of base position, averaged over a domain of adjustable size). Previous melts can be read back into MeltSim 1.0 for Windows, as well as any XY coordinate file one may wish to use for comparison or reference. Tm values can be calculated on any curve using an integration function. The value of Tm is displayed at the Tm on the graph along with a line. Curves and the melting map can be displayed scaled in various ways, and the window shows how the graph will look when printed.

MeltSim Related Software