Search Results for "dna sequence analysis" - Page 2
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Showing 396 open source projects for "dna sequence analysis"
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PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. You can download PFAAT from http://pfaat.sourceforge.net/
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# Digital Visual Computer (DVC) The Digital Visual Computer (DVC) is an experimental computing platform where programs and data are represented visually as images. This project contains the specifications, tools, and examples for the DVC ecosystem. ## Introduction DVC explores the concept of screen-to-screen computation. Instead of text-based code, DVC uses a "color language" where sequences of colors represent instructions (opcodes) and data. The state of the computer's memory is...
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gendasm
Generic Code-Seeking Diassembler with Fuzzy-Function Analyzer
...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. -
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ParDRe
Parallel tool to remove duplicate DNA reads
ParDRe is a parallel tool to remove duplicate reads. Duplicate reads can be seen as identical or nearly identical sequences with some mismatches. This tool will let the users to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset (e.g., assemblies, mappings, etc.). The tool is implemented with MPI in order to exploit the parallel capabilities of multicore clusters. It is faster than multithreaded counterparts (end of 2015) for the same... -
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PerfectSineWaves
Perfect and bit-perfect PCM encoded sine wave audio test tones
...This ensures clean looping and allows windowless FFT analysis. Each sinusoid in the file can have a unique phase and amplitude. The included wave file generation utility uses GNU MPFR library for extended precision floating point math and FFTW for verification. Output level is nearest possible to 0 dBTP without going over. -
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Jacobi-Static
STATIC/EX - simple multivariate statistics calculator
The STATIC/EX includes three applications: static.exe - a simple multivariate statistics calculator; spector.exe - file and online data viewer; tester.exe - an IPC client to develop and debug operations with embedded STATIC/EX IPC server. This toolkit can be used for: • user's training (who are interested in multivariate statistics) • scientific and other data researching. -
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OmicsSuite
OmicsSuite: a suite for multi-omics analysis and visualization.
OmicsSuite (https://github.com/OmicsSuite/, https://omicssuite.github.io), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to the development of bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multimomics (transcriptomics, genomics, protein omics, metabonomics, single cell), microbiology, clinical, etc. The program inherits the excellent interactive components, perfect analysis function and beautiful operation interface of HiPlot (https://hiplot.cn), which I developed based VUE.js and Node.js, etc. -
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OligoYap Portable
Oligo design and bioinformatic analysis software.
OligoYap can be used to design classical PCR, SYBR Green, TaqMan, MGB, Molecular Beacons, Microarray and Real-Time PCR primers/probes and for bioinformatics analysis. It has the features of enzyme cut analysis, mutation analysis, DNA/protein match and BLAST. You can easily record laboratory materials/files, prepare PCR mix and many other laboratory operations. It works on windows8.1 and earlier operating systems, but has not been tried on windows10 and later. For better images, you can right-click the exe file and check the features/compatibility "Disable screen scaling in high DPI settings" box. ... -
Peer to Peer Recognition Brings Teams TogetherCreate a positive and energetic workplace environment with Motivosity, an innovative employee recognition and engagement platform. With Motivosity, employees can give each other small monetary bonuses for doing great things, promoting trust, collaboration, and appreciation in the workplace. The software solution comes with features such as an open-currency open-reward system, insights and analytics, dynamic organization chart, award programs, milestones, and more.
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. ... -
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FastQC
A quality control analysis tool for high throughput sequencing data
FastQC is a quality control analysis tool designed to spot potential problems in high throughput sequencing datasets. Its goal is to provide a simple way by which to check the quality of raw sequence data coming from high throughput sequencing pipelines. It does this by running a modular set of analyses on one or more raw sequence files in fastq or bam format. It then produces a report summarizing the results, and highlighting any areas where the library may appear unusual. ... -
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Finding DNA Repeats by RFRE
RFRE is a tool to find DNA repeats (tandem and short)
A tool to FIND DNA REPEATS (tandem and short): RFRE is a mini tool to search for the repeated DNA sequences (SHORT REPEATS OR TANDEM REPEATS) characters by using the regular expression language (VB script). The Metacharcter and their behaviours in the context of regular expressions are the main methods to identify the different searched patterns and by different combination of Metacharcter, the programmed tool can search and detect the pattern of DNA sequence. ... -
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methylr
a single shiny solution from sequencer data to pathway analysis
Here we introduce methylR, a complete pipeline for the analysis of both 450K and EPIC Illumina arrays which not only offers data visualization and normalization but also provide additional features such as the annotation of the genomic features resulting from the analysis, pairwise comparisons of DMCs with different graphical representation plus functional and pathway enrichment as downstream analysis, all packed in a minimal, elegant and intuitive graphical user interface which brings the analysis of array DNA methylation data. -
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quantitative
Quantized transactions python3
...As an open-source educational resource, it’s designed for Python users interested in automatic trading, algorithmic strategies, and financial data analysis. -
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SGP AutoFocus LogViewer
Autofocus log viewer for Sequence Generator Pro.
This software extracts relevant autofocus data from the log files generated by the Sequence Generator Pro astrophoto capture software. It further allows to graph all the autofocus runs stored in the logfile and to calculate temperature coefficients and filter offsets. -
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Peptide Pattern Recognition
Software for non-alignment based analysis of DNA and protein sequences
Software for analysis, grouping and functional prediction of DNA and protein sequences as described in: Busk P.K. (2017). Peptide Pattern Recognition for high-throughput protein sequence analysis and clustering. BioRxiv. doi: https://doi.org/10.1101/181917. Busk P.K. and Lange L. (2013). Function-based classification of carbohydrate-active enzymes by recognition of short, conserved peptide motifs. -
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est-sfs
Estimate the unfolded site frequency spectrum and ancestral states
est-sfs implements a maximum likelihood method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities for DNA sequence data. The uSFS is a vector of counts of nucleotide sites with x derived allele copies in a sample of gene copies from a population. est-sfs infers the uSFS and ancestral state probabilities at polymorphic sites in a focal species using information from up to three outgroup species. Three models of nucleotide substitution have been implemented. ... -
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Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.
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PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative analysis, with a simple and intuitive graphical interface.
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. ... -
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EduData
Datasets in Education and convenient interface for dataset
Datasets in Education and convenient interface for downloading and preprocessing dataset in education. The CLI tools to quickly convert the "raw" data of the dataset into "mature" data for knowledge tracing task. The "mature" data is in json sequence format and can be modeled by XKT and TKT(TBA) The analysis dataset tool only supports the json sequence format. To check the following statical indexes of the dataset. In order to better verify the effectiveness of the model, the dataset is usually divided into train/valid/test or using kfold method. Each item in the sequence represents one interaction. ... -
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ASGARD
Metabolic reconstruction from DNA or protein sequences.
ASGARD is software for metabolic pathway reconstruction, but it can also generate other types of biological sequence annotation (EC and GO numbers, BLAST reports). This program is intended to be run in UNIX-like systems, and supports SGE or PBS. -
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GENET-CNV
Integrated DNA copy number variation and gene expression analysis
The Boolean implication networks outperformed Bayesian networks, Pearson’s correlation networks, and other Boolean networks in constructing genome-scale co-expression networks evaluated with comprehensive biological pathways and Gene Ontology in MSigDB. References: Guo NL, Wan YW. Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival. Artificial Intelligence in Medicine 2012 Jun;55(2):97-105. Ye Q, Singh S, Qian PR, Guo... -
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RESTAMP
Microbial division rate and death rate estimates.
RESTAMP - Rate Estimates By Sequence Tag Analysis of Microbial Populations, is an analytical framework for estimating microbial division rates and death rates. It consists of Matlab based software for producing founder population size values from next-generation sequencing data. It also includes scripts that implements the equations that determine the rates from CFU and founder population size values. -
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Citrus
Citrus: Editing HiC data for de novo genome assembly
juicer and 3D-DNA are two tools that re-arranges HiC data (xxx.hic format) and splits/re-orders super-scaffold data (xxx.assembly) to improve de novo genome assembly. Juicebox was specifically designed to tune or adjust genomic sequences based on HiC data. However, the current Juicebox version does not have a function to save updated HiC data and to summarize chromosome sequences. Thus, we created Citrus which can edit super-scaffolds according to chromatin conformation data captured in...
