Search Results for "dna database"
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Showing 39 open source projects for "dna database"
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RedDiamond
Text editor supporting EDT keypad navigation
This began as a fork of the Diamond text editor. It now shares very little DNA with Diamond because it uses CsScintilla edit widgets and has many more features. EDT keypad navigation, themes, configurable backup history, along with many other improvements have happened. Project still uses CopperSpice cross platform library. Linux users upgrading from older versions to 3.5.8 or later should cd .local/share rm -rf LogikalSolutions rm -rf LogikalSolutions-RedDiamond/ rm -rf ~/.config/LogikalSolutions-RedDiamond/ Due to database changes. -
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MolMarker
Java software to evaluate the results obtained by molecular markers
Journal article to cite: Jahnke, G.; Smidla, J.; Poczai, P. MolMarker: A Simple Tool for DNA Fingerprinting Studies and Polymorphic Information Content Calculation. Diversity 2022, 14, 497. https://doi.org/10.3390/d14060497 Leave a review, please! Your opinion matters! :-) MolMarker is user-friendly software to help evaluate the research results obtained by molecular markers. The software can handle genetic (e.g. SSR) and biochemical (e.g. isozyme) data, can construct similarity... -
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Damage-Net
Program for meta-analysis of large-scale datasets into DNA-repair.
Welcome to Damage-Net! This page is no longer in use, please go to our very own website from now on! www.damage-net.co.uk Our websites has all the latest info, downloads and updates. -
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GMATA software for Genomic SSR marker
Genome-wide Microsatellite Analyzing Toward Application: GMATA
...It is also cross-platform and supports Unix/Linux, Win and Mac. Results from software GMATA can be directly graphically displayed with genome or gene features in Gbrowser and easily integrated with any genomic database. -
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GelJ
GelJ is a Java program for the analysis of DNA gel fingerprints images
GelJ is a Java application designed for analysing DNA fingerprint images. GelJ is a feather-weight, user-friendly, open-source and free tool that combines the simple design of free systems with instrumental features for DNA fingerprinting that are only available on commercial tools. Some of the outstanding features of GelJ are functionality for accurate lane- and band-detection, several methods for computing migration models and generating dendrograms, comparison of banding patterns from different experiments, and database support. ... -
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epidaurus
tumor epigenetic database
Epidaurus is a collection of epigenetic datasets including transcription factor ChIP-seq, histone ChIP-seq, DNase-seq, FAIRE-seq, DNA methylation, etc. It also includes commonly used genome features (GC content, conservation) and RNA-seq. A user friendly interface has been developed to interrogate and visuzlize these datasets. -
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FHiTINGS
Fungal High-throughput Taxonomic Identification tool for use with NGS
FHiTINGS is designed for use in rapidly identifying, classifying, and parsing internal transcribed spacer (ITS) DNA sequences after a BLASTn search. This software is useful for fungal ecology studies using next generation sequencing (NGS). See our paper in the Journal of Basic Microbiology (http://onlinelibrary.wiley.com/doi/10.1002/jobm.201200507/pdf) for more information and please cite that paper if you use our program. Thank you for using FHiTINGS! -
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HTSFinder
High-Throughput DNA Signature Finder
HTSFinder consists of three computational phases. This pipeline generates all the possibilities of k-mers for every genome individually and then determines their frequency in the entire database. Finally, DNA signatures of every species or strain are obtained in the database or multiple databases that have been involved in the pipeline. HTSFinder implements the parallel and distributed computational tool Hadoop for the second and third phases. -
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HitKeeper is a database application for use in BioInformatics. It deals with "hits" (predicted features) on biological sequences (protein, DNA), handles incremental updates effectively, supports taxonomy, and provides original query tools.
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MPprimer
a program for reliable multiplex PCR primer design
...It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. -
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RAPSearch2
Reduced Alphabet based Protein similarity Search
RAPSearch2 is a tool for fast protein similarity searches. RAPSearch2 searches short DNA sequences (reads) or protein sequences against protein database, achieving >100 times speedup as compared to BLASTX (for reads of ~100bp), or >1000 times speedup over BLASTX in the accelerating mode (option "-a"). RAPSearch2 utilizes reduced amino acid alphabet and flexible seed so that seeds of various lengths with mismatches can be identified quickly by hashing. -
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MSRE-HTPrimer
A high-throughput primer design tool for MSRE-assay in epigenetics
MSRE-HTPrimer is an open-source, portable, web-based and easy-to-use tool, which facilitates the design of primer pairs for epigenetic assay design and and genomic sequencing assay design. It uses a simple input and output model and can design primers for hundreds to thousands of target sequences in a single run. Moreover, it does not have any limitations on the number and size of target sequences. MSRE-HTPrimer provides significant improvements over existing solutions with following unique... -
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To speed up the alignment of DNA reads or assembled contigs against a protein database has been a challenge up to now. The recent tool DIAMOND has signi cantly improved the speed of BLASTX and RAPSearch, with a similar degree of sensitivity. Yet for applications like metagenomics, where a large amount of data is involved, DIAMOND still takes too much time. We introduce AC-DIAMOND, which attempts to speed up DIAMOND via better SIMD parallelization and reference indexing. ...
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DW2 Digivolver
Make your Digimon World 2 gameplay a lot easier.
DW2 Digivolver is a JAVA developed software that aims to facilitate the creation of your Digimon World 2 team throughout the game. The software tries to create a friendly interface for the user to discover the easier ways to get a wanted Digimon via the DNA Digivolution system using an extensive database. On future work, the software is to be updated to become a full support tool for playing Digimon World 2, extending the database to cover Skills, Stages, Items and more. -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
Very simple python script which saves you the pains of counting the amino acids/DNA bases in fasta files from the Uniprot and NCBI RefSeq Database (1, 2). Lets say you want the amino acid sequence of range 128-387 from a 1000 amino acid protein - this script will help you to avoid counting mistakes by just showing you the specified sequence in amino acids and coding DNA base pairs (ideal for amplification primer design) of a specified Uniprot ID -
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Gecko Hamaker
Calculates Hamaker coefficient,interaction free energy,force,torque.
The Gecko Hamaker open-source software project is a full implementation of the fully retarded Lifshitz formulations for isotropic and anisotropic plane-plane and cylinder-cylinder interactions with intervening interlayer materials, planar systems of up to 99 layers, and graded interfaces for the modeling of grain boundaries or other continuously changing systems, accompanied by a database of material optical properties spectra. The machine-readable optical property database is available... -
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VarImpact
Extracting effects of mutations on molecular properties from text.
Genetic variants alter cellular behavior in a variety of ways, changing biochemical properties of DNA, mRNA, and proteins. Many large-scale sequencing projects are under way to detect human variation in health and disease. Although broad disease associations can be discovered by GWAS studies, the low-level impact of mutations is hardly available in structured form. The results of thousands of small-scale experiments, on the other hand, are present in the literature and discuss observations... -
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Qudaich
Performs local sequence alignment for NGS data
Qudaich (queries and unique database alignment inferred by clustering homologs) is a software package for aligning sequences. Qudaich generates the pairwise local alignments between a query dataset against a database. The main design purpose of qudaich is to focus on datasets from next generation sequencing. These the datasets generally have hundreds of thousand sequences or more, and so, the input database should contain large number of sequences. -
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GenomeRunner
Annotation and enrichment of Next-Gen sequencing data
Note: This version requires additional SQLite database files. Contact the developers to obtain them. Use http://www.integrativegenomics.org/ for the latest data and analyses. GenomeRunner is a tool for automating genome exploration. It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser. Input - any genome-wide data data in .bed... -
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Clover
a simple lab information management system (LIMS)
Clover is a simple lab information management system (LIMS) designed for biology labs, especially plant biology labs. It provides an easy way to manage and handle the information of lab material, catalogs (inventories), and orders. USE PHP 5.*! Clover will not work on PHP 7.*! The wiki page contains detailed help documents: https://sourceforge.net/p/cloversystem/wiki/Home/ For lab instrument scheduling, please use Cloveriver: https://sourceforge.net/projects/cloveriver/ Please... -
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CDSbank
multi-sequence extraction, filtering & formatting
CDSbank is a database that stores both the protein-coding DNA sequence (CDS) and amino acid sequence for each protein annotated in Genbank. CDSbank also stores Genbank feature annotation, a flag to indicate incomplete 5’ and 3’ ends, full taxonomic data, and a heuristic to rank the scientific interest of a species. This rich information allows fully automated data set preparation with a level of sophistication that meets or exceeds manual processing. -
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DMEAS
DNA Methylation Entropy Analysis Software
DMEAS (DNA Methylation Entropy Analysis Software) is written in C# language. It is a user-friendly DNA methylation analysis tool for DNA methylation pattern visualization and extraction, DNA methylation level calculation and DNA methylation entropy analysis. DMEAS progressively scans the mapping results of bisulfite sequencing reads to extract DNA methylation patterns for contiguous CpG dinucleotides. It was developed in order to assess the DNA methylation variations within a cell population... -
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u/sbmv2012
Taxonomy assignment of metazoans using a python based pipeline
The aim of this project is to create an automated pipeline for taxonomic assignment of DNA sequences obtained from environmental samples. We develop a series of python scripts to process the raw sequence data obtained from benthic environmental samples and to taxonomical assignment of these sequences and finally to integrate all data in a relational database. -
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Primer Design Tool
Design PCR primers
A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them. -
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MSDB
Microsatellite Search and Building Database
MSDB (Microsatellite Search and Building Database) is specially designed to offer you a user-friendly interface for finding microsatellite markers, their exact position and frequency of occurrence from genomic sequence. MSDB can accept large number of sequences in GenBank, FASTA and EMBL formats as input and large number of motifs can be searched simultaneously. The program not only can search pure microsatellite but also can search compound and complex microsatellite. The outputs are...
