Search Results for "alignment" - Page 13
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Showing 522 open source projects for "alignment"
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erne
ERNE - Extended Randomized Numerical alignEr
We present ERNE (Extended Randomized Numerical alignEr), a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE comprises ERNE-FILTER (read trimming and continamination filtering), ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), and ERNE-PMAP/ERNE-PBS5 (distributed versions of the aligners), -
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PolyRec
Unistroke gesture recognizer
...More technical details on PolyRec can be found in the following scientific paper: V Fuccella, G. Costagliola; Unistroke Gesture Recognition Through Polyline Approximation and Alignment; in Proceedings of CHI 2015; pp. 3351-3354 http://dl.acm.org/citation.cfm?id=2702 -
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Phylomark
Identification of phylogenetic markers from whole genome alignments
Phylomark is a python script used to identify phylogenetic markers from whole genome alignments. Accurate phylogenetic markers are chosen based on low Robinson-Foulds distance to a phylogeny inferred from the whole genome alignment. -
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MeSeq is a package providing ease in installing some popular Multiple Sequence Alignment Tools. It also provides a GUI interface for the tools.
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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.
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RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
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RASTools
A tools package for short reads alignment show
A tools package for short reads alignment show -
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BNP-Homology
Alignment data for Protein Remote Homology Search
Alignment data from the application of a Bayesian mixture model to protein remote homology detection. -
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libmusical is a c++-software library that provides classes and functions for alignment of sequences of symbols. The intended field of application is the alignment of musical sequences for Music Information Retrieval purposes.
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PROMOT
A tool for finding functional motifs from aligned protein sequences
...To run the tool, you need to have Java 8 installed on your system. Download and execute the JAR without any parameters to know about how to use the tool. A sample alignment of 91 protein sequences is also provided in the file "aligned.fasta". A sample run of the tool can be seen by using the following command: java -jar promot4.jar 70 2 n aligned.fasta > output.txt The above command sets fitness threshold to 70%, number of choices per motif element to 2, and ignores the functional grouping of the amino-acids, asking to input the data from aligned.fasta and redirecting the tool output to output.txt. ... -
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lxnstack
A program to align and stack astronomical images.
...) * Two automatic align method: align-points; phase correlation, * One manual align method. * sub-pixel precision (0.1 pixel for phase correlation and 0.01 pixel for manual alignment). * Automatic image derotation. * FITS file support (by installing the python2 package 'astropy') * Hot pixels suppression algorithm * CR2 files native support * Can load/save video * Grayscale RAW image support * Editing of result image's levels. * Light curve generation -
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biosbl
Standard Bioinformatics Library
set of classes used to handle input/outputs of bioinformatics data files and basic operations as multiple alignment and phylogenetic reconstruction. -
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ncmock
NetCDF mock data generator.
...Variables can be any type and filled with data in 5 ways, either a constant, a checker pattern, randoms, linear range, or a sombrero ripple function, all of which can be animated too if they use a record dimension. Global and variable attributes can also be created. Esoteric controls exist for choosing alignment, blocksize, file flavor (classic or HDF5), prefill, initial size, and header pad. ncmock has throughput and peak memory calipers, so it can also be used as a benchmark tool -
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LAMSA
Long Approximate Matches-based Split Aligner
LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and good ability of handling SV events. It is well-suited to align long reads (over thousands of base-pairs). -
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This is an R package for the Mass spectrometry Research. The MrR can be used to analyze the mass spectrometry data for baseline correction, denoising, peak detection, peak alignment, peak normalization, and biomarker discovery.
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vim-easy-align
A Vim alignment plugin
vim-easy-align is a Vim/Neovim plugin that makes it simple to align text by a pattern, character, or regular expression across a selection or motion. Instead of hand-inserting spaces and fiddling with tabs, you select lines and invoke an interactive prompt that previews the alignment as you type the rule. It supports multiple delimiters—commas, colons, equals signs, pipes—and can align on the nth occurrence or on complex regex groups. The plugin is designed to be composable with normal Vim workflows, working in visual mode or with motions, and honoring your indentation and tab settings. It also offers left, right, and center alignment, plus padding and justification control, so tables, hashes, assignment lists, and Markdown fragments look neat. ... -
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Software for visualization of point variability in pairwise sequence alignment FASTA format. Featuring GUI interface, this simple application enables insight into variation of nucleic and amino acids on specific loci. Current 1.1 version supports amino and nucleic acid alignments. There are 2 variations of this software. One is CLI based and the other one is GUI based. Read corresponding README files in order to get familiar with the software.
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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. Visit http://www.biomedcentral.com/1471-2164/15/858/abstract for the pdf article describing the utility of iMSAT and if you use the program please cite this article as: Andersen and Mills: iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina libraries. ...
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The"Amip" GUI is intended to provide code examples of the methods proposed in: "Unsupervised image segmentation for microarray spots with irregular contours and inner holes" authors: Bogdan Belean, Monica Borda, Jörg Ackermann, Ina Koch and Ovidiu Balacescu Journal: BMC Bioinformatics, 2015, 16:412 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0842-3 PDE were used for grid alignment, whereas autocorrelation driven PDE and k-means clustering were used for spot segmentation. The proposed segmentation procedure yields the spots median intensity values for the microarray images recorded from Cy3 and Cy5 fluorescent dyes. Based on the fold change factor, the differentially expressed genes were determined. ...
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StockSims Inspector Simulator
StockSims Inspector Simulator
Stock Price Inspector Moon Phase Alignment Inspection Trading Simulation Engine Key View (Multiple Time Frame Comparator) -
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MicroRNA_alignment_evaluation
MicroRNA alignment Supporting Data
The scripts and sequence files deposited here are supporting information to our recently submitted paper that investigates the accuracy of NGS aligners for microRNA studies. -
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Telomerecat: The Telomere Computatioanl Analysis Tool Telomerecat allows you to generate average TL estimates for any high throughput paired end sequencing samples.
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HBS-tools
a set of tools for hairpin bisulfite-seq data analysis
...Here we present HBS analyzer, the first command line based open-source tool to process genome-wide hairpin bisulfite sequencing data. It accepts Illumina paired-end sequencing reads as input, performs alignment to recover the original (pre-bisulfite-converted) DNA sequences and calls methylation status for cytosines on both DNA strands. -
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sam_comp
Compression for SAM/BAM file format
This is a simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. -
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CUSHAW3 is an open-source parallelized, sensitive and accurate short-read aligner. This aligner proposes a general approach to properly aligning both easy and hard reads to large genomes such as the human genome. Perform evaluation on alignment quality reals that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novalign3 for short-reads with high error rates.
