Search Results for "align" - Page 6
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Showing 174 open source projects for "align"
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TMX editor
Open, edit .tmx files and set specific metadata
Open, edit .tmx files and set metadata to make them of better use in the most CAT programs. Very light program written in C++, enables you to open (almost) any types of bilingual .tmx file, edit it, split and merge segments, shift the segments up and down as well as delete them. In-built QA checker helps to identify wrong alignments. The most important is the ability to add and edit metadata - proper ones as well as those embodied in opened tmx. Finally you can save the TMX in a... -
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New version was released! Visit https://github.com/jsnjack/simpleblogger to download Simple Blogger is a small and very easy to use application that enables you to quickly write and publish a new post of your blog. Available in Windows and Linux. Simple Blogger has written on Python with wxPython.
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RDP FrameBot is a frameshift correction and nearest neighbor classification tool for use with high-throughput amplicon sequencing. It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline, tutorial http://rdp.cme.msu.edu/tutorials/framebot/RDPtutorial_FRAMEBOT.html. ...
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calc2booktab.latex
Script for OpenOffice/LibreOffice to convert tables to Latex-Code
UPDATE: The project was moved to github (https://github.com/schober-ch/calc2booktab). The soruceforge page won't get any bugfixes, please use the github repo if you want to try this macro. -------------------------------------------------------------------------- A Python extension for OpenOffice/LibreOffice to convert selected cells to LaTeX-Code. Its similar to Calc2Latex, but typographic formatting is more advanced (numeric columns, dcolumn-package, booktab-package) Script is... -
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FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a... -
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GLProbs
GLProbs: Aligning multiple sequences adaptively
GLProbs is a simple and effective approach to improve the accuracy of multiple sequence alignment. We use a natural measure to estimate the similarity of the input sequences, and based on this measure, we align the input sequences differently. To test the effectiveness of this approach, we have implemented a multiple sequence alignment tool called GLProbs and compared its performance with a dozen leading alignment tools on three benchmark alignment databases, and GLProbs’s alignments has the best scores in almost all testings. We have also evaluated the practicability of the alignments of GLProbs by applying the tool to three biological applications, namely phylogenetic trees construction, protein secondary structure prediction and the detection of high risk members for cervical cancer in the HPV-E6 family, and the results are very encouraging. -
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blastplot
A simple and easy to use perl package to plot blast output results
...Read-based BLAST analysis of NGS data is a common procedure especially in the case of metagenomic samples. However, coverage is usually not enough to allow for de novo assembly. This type of read-based analysis often creates the question of how a set of reads that align to the same sequence is distributed. The same question applies to preparation of primers or probes for microarray experiments. We have created BLASTPLOT, a PERL module to quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. BLASTPLOT is a simple to use PERL module that allows the generation of PNG graphs for all the reference sequences associated with a BLAST result set. ... -
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A free computer-aided translation / computer-assisted translation (CAT) tool to align and converter bitext into TMX translation memory format to be used in other CAT tools by translators and other language professionals.
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SOAPindel2
SOAPindel2 focusing on calling indels from the next-generation p
Requirements SOAPindel2 needs two input data sources: The reference sequence file used to align the reads. It must be in Fasta format. The files with read-alignments. SOAPindel2 accepts only Indexed BAM formats as input. Users can use the tools/soap2sam.cc to convert SOAP format to SAM format and use samtools convert SAM to indexed BAM. SOAPindel2 can guess the library insert sizes by itself. Sequencing platform:Theoretically, SOAPindel2 is designed for all paired-end sequencing data because it doesn’t consider any qualities for now. ... -
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Qudaich
Performs local sequence alignment for NGS data
...Qudaich is flexible and its algorithmic structure imposes no restriction on the absolute limit of the acceptable read length, but the current version of qudaich allow read length <2000 bp. Qudaich can be used to align DNA, translated DNA and protein sequences. -
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iAstroDroid
Automated astrophotography on Android
iAstroDroid is a world first solution for controlling the autoguider, CCD, DSLR, and mount for astrophotography on Android devices. iAstroDroid run on a parallel OS (Chroot) on an Android device. A user can control all devices via a web browser on Android. Requirements and supported devices. 1. Autoguider: QHY5 or QHY6 2. CCD: QHY8L 3. DSLR: Canon or Nikon DSLR 4. USB serial adapter (FTDI232) for controlling a DSLR camera shutter and a serial shutter... -
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tisa - Tab Indent Space Align
A program that will correct both indentation and alignment.
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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Ferox
Ferox - Sequence Alignment with Fuzzy K-mers
Ferox is a DNA sequence alignment application that uses fuzzy k-mers to quickly and accurately align sets of sequence reads against a reference genome. Ferox can also be used to align whole genomes. The seeding mechanism used by Ferox is highly configurable, allowing custom fuzzy seeds to be created declaratively in an XML configuration file. -
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CGAP-Align
A new time efficient read alignment tool built on the top of BWA
See Wiki page for details. -
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ClovisGrid
Simple grid overlay that runs over SWTOR.
This program runs a simple grid that displays over SWTOR to allow you to more easily align your GUI with the new patch 1.2 interface editor. New with version 1.3: - Visibility-toggle hotkey (ctrl+shift+home) - Snap cursor to grid! (to toggle, hold ctrl+shift+tab) V 1.3.a - Fixed several problems occurring at certain resolutions. -
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graphICs
graphICs is a converter transforming GDS II-data to Asymptote-code
...This code can be translated via Asymptote to PDF, PNG or other formats. The output can be specified to be printed on an A-format paper, portrait or landscape, top/right, center or bottom/left align. To use graphICs you need to download the JAR-file containing the program (no installation needed) and the MAP-file containing the color-information for the design (you can modify it or you create your own). To create graphic or PDF-files you need to download Asymptote from asymptote.sourceforge.net. Look at http://sourceforge.net/p/graphicsic/wiki/Usage/ for the Usage. ... -
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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This project has been moved to https://github.com/loomchild/maligna . All further development will be done there.
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<img src="http://etudiant.univ-mlv.fr/~ofiguero/anaconda_logo_2.gif" align="right" /> A java based file navigator/manager to be used on both Linux and Windows OS
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Vehicle Alignment Tool for Simutrans
Vehicle Alignment Tool for Simutrans
This tool allows Simutrans artists or pak mantainers to better align their vehicles by showing a preview of a convoi for each of the eight Simutrans views. This tool is thought to provide a quick way to fix those small glitches affecting multiple vehicle convois. The individual vehicles can be selected, moved and saved, all in a real-time preview environment. -
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EGallery
A simple PHP image gallery with cache and no database.
...Features include: - Cached thumbnails to reduce page load times - Upload script to add image files from your web browser - Download all images as a .zip file - Clicking on an image thumbnail prompts users to save the original image file to their computer Credits: - Utilizes the jQuery Masonry plugin to align images: http://masonry.desandro.com/ - Upload script from Uploadify: http://www.uploadify.com/ - Thumbnail creation: http://code.google.com/p/timthumb/ -
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JFinisher
JFinisher is software for alignment, editing and manipulation DNA seqs
JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and ability to export results in the standard formats of the area. -
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A GUI program to create the plasmid database forms for BGME lab. This program presents user with a data entry form for entering plasmid information and automatically converts DNA sequence to protein, aligns it, and creates text output file.
