Search Results for "dna sequence analysis"

...It allows you to enter known starting vectors for a given code image for the micro. It will disassemble the code and follow through branches to assist in the separation of code and data. Its included Fuzzy Function Analyzer companion uses a DNA Sequence Alignment Algorithm to locate similar code in multiple binaries to facilitate reverse-engineering and/or code recovery. The original purpose of the Fuzzy Function Analyzer was to assist in code recovery where the source code for the current binaries got lost, yet the source code for an old binary was retained. The Fuzzy Function Analyzer allows you to match up known functions between the two binaries so you can concentrate on disassembling and reverse engineering the parts that are different and recover the code for the current binary that got lost.

The M6811 Code-Seeking Disassembler is a command-line tool that lets you enter known starting vectors for a given code image for the 6811 micro. It will disassemble the code and follow through branches to assist in the separation of code and data. Its companion Fuzzy Function Analyzer uses DNA Sequence Alignment Algorithms to locate similar code in multiple binaries, facilitating reverse-engineering. Originally written to analyze code from GM automotive engine controllers, but is useful anywhere a 6811 micro is being used. Version 1.0 was written in Borland Pascal in April 1996, and updated to v1.2 in June 1999. ...

The goal of this project is to provide a generator for lexical analyzers of maximum computational efficiency and maximum range of applications. This includes the support for Unicode (UTF8, UTF16, ...) and a large variety of other encodings directly and via nested converters such as ICU(tm) and IConv. Sophisticated buffer handling allows to operate on plain file streams, on sockets, or manually fed buffer content. 'Ready-to-build' examples explain related concepts and facilitate practical...

TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS.

KMWin (Kaplan-Meier for Windows) is a convenient tool for graphical presentation of results from Kaplan-Meier survival time analysis. The programme is based on the statistical software environment R and provides an easy to use graphical interface. As an introduction, see http://dx.plos.org/10.1371/journal.pone.0038960#s2.

Recent advances in DNA cloning and synthesis technologies afford high throughput implementation of designed sequences into living cells. However, our ability to design sequences to interrogate multifactorial biological processes and further engineer biological functions is lagging behind. DNA-Tailor (D-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design.

HPeak is a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites. Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl...

BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions.

EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)

EXPR is a software package for the recording and analysis of animal behaviour. Recording is done by pressing particular keyboard keys on the computer. The software then saves the sequence and timing of behaviours. Note that the DOS (1995: https://sourceforge.net/projects/expr/files/expr/fb-port-expr-00-1995/EXPR-binary-DOS-0.0.1995.tar.gz/download) version is currently the only fully functional and is recommended for use.

Lucy is a program for DNA sequence quality trimming and vector removal. Its purpose is to process DNA sequence data acquired from DNA sequencers to prepare the data for downstream processing applications such as genome assembly.

mccore is a bioinformatics data structures and tools library for efficient analysis and manipulation of RNA, DNA and protein 3D structures.

FlexCRFs: A Flexible Conditional Random Fields Toolkit for Labeling and Segmenting Sequence Data (this includes a parallel implementation of CRFs called PCRFs to support training CRF models on massively parallel computer systems).

The set of tools for biopolymer sequence analysis together with GUI to work with biopolymer sequence databases. The tools include pairwise and multiple alignment, philogenetic tree construction and other.