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Showing 24 open source projects for "repeat"
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Image16
Image viewer/editor specialized in astrophotography 16bits processing
Opens/saves TIF, FITS, PNG, XISF, PXM, RAW, JPG, XCF, PSD. AsinH, Sqrt, Ln, Exp and Sqr stretching, HSL and RGB adjusting, Levels and Curves adjusting and Background Extraction for Color Balance, Flatness and Gradient Correction. Arithmetic between images. Resizing and croping. Color Balance based on background, selection or stars B-V (after platesolving). Debayering/Bayering. Inversion, mirroring, rotation, barrel/pincushion correction. RGB alignment/shifting. Erode, Dilate, ... Blurring... -
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Text File Generator
Generate large text files for various testing purposes
... them repeat occasionally. -
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Universal-mer
A CLI tool for k-mer counting with all possible sizes of k at once
Universal-Mer is a k-mer counting tool for all possible size of k at once. More than typical k-mer counting tools, the program can summarize the exact counting result of 1-mers to l-mers at once where l = the length of longest repeated substring in the input sequence where now the maximum length is set to 100000-mers. The program can report exactly the number of all repeat (freq>1) and unique(freq = 1) mers , and the number of all possible substrings of sequences without cutting off any low... -
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adcptools
Set of functions to process acoustic Doppler current profiler data
adcptools is a set of Matlab functions to post-process acoustic Doppler current profiler data. It consists of several low-level function to read out data files and several functions to process data from repeat transect measurements, moored turbulence measurements and horizontal ADCP deployments. -
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detectMITE
Detection of Miniature Inverted Repeat Transposable Elements
detectMITE - a MATLAB-based tool for detecting miniature inverted repeat transposable elements (MITEs) in genomes. [1] Who are we? Please visit website: http://bioinfolab.miamioh.edu [2] How to cite detectMITE? Ye C, Ji G, Liang C (2016) detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes. Sci. Rep. 6, 19688. http://www.nature.com/articles/srep19688 Ye C, Ji G, Li L, Liang C (2014) detectIR: A Novel Program for Detecting Perfect... -
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AAARF, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in a genome.
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iMSAT represents a full update of the vcf2MSAT program. This command line python program allows for a user to use the polymorphism data generated using SAM- and BAM-tools and a .fasta alignment file to search for polymorphic microsatellite markers (MSATs or STRs). By identifying polymorphic makers, rather than simple repeat regions as previous programs have done, iMSAT greatly increases the speed at which polymorphic MSATs that can be identified -- saving researchers precious time and money...
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mitoMaker
mitoMaker - a mitochondria pipeline wrapper script
... pipeline started to appear: assemble reads with MIRA or SOAPdenovo-Trans, look for a scaffold/contig that matches a closely-related species, check it to see if all expected genomic features are present (since mitochondria is well conserved), check to see if the assembly might have circularized (since it's a circular DNA). If a feature was missing, or it hasn't circularized, try and assemble again with different assembler parameters (mainly k-mer). Rinse and repeat until the best build is found. -
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primeScaff is intended to automate the sometimes tedious process of manually designing specific primer pairs around gaps of genomic scaffolds and speedup the genome finishing stage of a genome sequencing project. It incorporates de-novo repeat finding using RECON to avoid as much as possible designing primers in repetitive regions and offers the possibility to easily fine-tune the primer design options using primer3. It outputs the repeat, gap and primer annotations in gff2 and gff3 to easily...
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easyPAC
easy Primer prediction from Alignments and Consensus sequences
Primer prediction from alignments and consensus sequences. easyPAC applies all standard quality tests to degenerate primer and primer pairs and optionally maps all primer candidates to an arbitrary number of reference files like repeat databases or genomes to ensure target specifity. -
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Boundary Shift Integral
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Project Chronos
Chronos
UPDATE, Check out our new website where we will host all future updates and improvements. The Sourceforge site will no longer be maintained and updated. www.TheChronosProject.com Project Chronos is an open source time lapse rail. It is a fully features system that offers the same level of control as professional systems costing thousands of dollars. It is also the most accurate time lapse system available capable of making accurate movements 1/125th the width of a human hair. And the... -
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Multiple Alignment Manipulator
MaM processes and manipulates multiple sequence alignments.
MaM is a software tool that processes and manipulates multiple alignments of genomic sequences. MaM computes the exact locations of common repeat elements in multiple aligned sequences, provided by a variety of user identified programs databases and tables. It then graphically displays how the alignment quality varies throughout the aligned sequences, providing separate displays for the repeat and non-repeat portions. -
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Console based notepad number cruncher makes calculations fast and simple, yet with ample features under the hood. With log turned on, you can record your session on-the-fly from any open instance of the program.
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MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
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JNC CR ICICS 2011
Joint Network Coding for Interfering Wireless Multicast Network
In this paper we propose a Joint Network Coding based Cooperative Retransmission (JNC- CR) scheme, where we show that ANC along with DNC can offer a much higher retransmission gain than that attainable through either ANC, DNC or Automatic Repeat reQuest (ARQ) based retransmission. -
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RIPCAL is a bioinformatics tool for the analysis of repeat-induced point mutation (RIP) of fungi. If you publish work using RIPCAL please cite: Hane & Oliver, BMC Bioinformatics 2008, 9:478
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FONZIE is a bioinformatic tool written in Python developed for the genetic cartography speciality. FONZIE allow as well to find markers on a set of sequences than to find associate oligonucleotides. http://www.biomedcentral.com/1756-0500/3/322/abstra
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Whole-genome scale multiple genome local alignment search program. Supports unlimited length gapped-seed patterns, parallelization through distributed hashing, and unique a TF-IDF based repeat filtering method.
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STR miner(or SSRdigger) is a SSR searching software which supports both perfect and imperfect SSR search with specified length, match percentage and repeat threshold. With a GUI interface, fasta and MS excel format output, STR miner is user-friendly.
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RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats. Radar has moved to github (https://github.com/AndreasHeger/radar)
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D. R. Kaprekar found an interesting behaviour of four-digit number (say, 6349). Take any number; sort its digits in ascending (3469) and descinding (9643) order; subtract these (9643 - 3469 = 6174). Repeat these steps a couple of times. Surprisingly, you'
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Open ERPS allows patients to be able to register, login and request new repeat prescriptions and make use of Healthcare services. The system allows users to quickly configure an effective web info service including services eg: Collection Service
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The Tandem Repeat Occurrence Locator -- TROLL -- is a light weight SSR finder based on a slight modification of the Aho-Corasick algorithm.
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