Search Results for "alignment" - Page 16
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Showing 522 open source projects for "alignment"
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DNAA is the DNA analysis package, for analyzing next-generation post-alignment whole genome resequencing data. Specifically, DNAA is able to find structural variation, SNP and indel variants, as well as evaluating the mapping and data quality.
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DNase2Hotspots
This software identifies tag-enriched regions(hotspots) from DNase-seq
DNase2Hotspots is a software package for identifying tag-enriched genomic regions (hotspots) from the DNase-Seq genomic data. This program reads a BAM (Binary Alignment/Map) file or tab-delimited text files as input and produces a list of hotspot candidates and associated z-scores as output. Mappability profiles for the reference genome and genomic regions of repeat maskers are also required as input. -
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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 semi-supervised anomaly detection strategy based on logistic regression. ... -
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DimerRemover
Remove adapter dimers from NGS data
...Using a provided adapter sequence, it generates variations of this sequence and stores them in a hash table. The reads can then be directly matched against the hash. It is far more time efficient than doing alignment. -
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INDI alignment infrastructure
N point alignment infrastructure for INDI telescope drivers
This project is no longer under active development. It has been superceded by the alignment subsystem which is now part of the main INDI project. This project provides an "alignment layer" driver to sit above INDI telescope drivers. This layer performs transformation services for telescope coordinates as they pass up and down to the underlying driver. The conversion matrices are computed from alignment datums passed down into the alignment layer. ... -
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Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.
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The AAT (Analysis and Annotation Tool) spliced genome alignment package now available as Open Source.
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t2t-pipe
automatic alignment pipeline for parallel treebanks
The *Tree-to-Tree (t2t) Alignment Pipe* is a collection of python scripts, co-ordinating the process of automatic alignment of parallel treebanks from plain text files with a single call from a unix command line. Supported Languages: DE, FR, EN -
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RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files.
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Ship Agents FasterGemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
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Cylindrical BLAST Viewer
Alignments in Rotating Cylinder / 3D
3D viewer which arranges BLAST hits and other bioinformatics-related alignments in a rotating, cylindrical display. Feedback appreciated. NOTE: requires Java3d installation. Superceded by Cylindrical Alignment App -
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A protein alignment curation tool using Local Covariation from "Protein Sequence Alignment Analysis by Local Covariation: Coevolution Statistics Detect Benchmark Alignment Errors" by Dickson et al. published in PLoS ONE on June 8, 2012.
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The sequence alignment task in MAGI (magi.ucsd.edu) is based on the miRanda algorithm, but we redesign the miRanda algorithm on GPU by taking its advantages of massively parallel computing and extra high memory bandwidth using using NVIDIA’s Compute Unified Device Architecture (CUDA). The CUDA-miRanda implementation is a fast microRNA target identification algorithm that aligns short nucleotide sequences (i.e., < 32 nucleotides) against longer reference sequences (e.g., 20k nucleotides). ...
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LatexRender-ng is the new generation of the popular LatexRender, a filter that will render LaTeX fragments into images. It includes many enhancements to LatexRender, including the correct alignment of the images with respect to the baseline and svg.
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MSA-CUDA: multiple sequence aligner
multiple sequence alignment on CUDA-enabled GPUs.
This project is not active any more since we failed to get the permit from the Clustal team to distribute our software. You can refer to the paper "Yongchao Liu, Bertil Schmidt, Douglas L Maskell:MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA. ASAP 2009" for more details. -
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OrthoRBH
Rapidly identify orthologous cDNA sequences in related species
...It is suited to handling a mixture of EST and mRNA-seq sequence data. It performs batch blast searches, so it is ideal for large multi-gene families. After collecting candidate sequences, it performs sequence alignment and deposits sequences into a fasta sequence file for downstream molecular evolutionary analysis. -
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Normalize.css
A modern alternative to CSS resets
...Rather than a “hard reset” that zeroes everything, it preserves sensible defaults for elements while fixing inconsistencies and edge cases that vary between engines. The project documents why each rule exists, targeting real-world quirks such as form control alignment, typographic defaults, and HTML5 element rendering. It is deliberately minimal and stable, making it a safe foundation for both custom design systems and heavyweight frameworks. Because it normalizes only what’s necessary, it plays well with component libraries and avoids surprising overrides that can lead to fragile CSS. Teams adopt it to reduce cross-browser bugs, speed up layout work, and start with predictable typography, spacing, and element behavior. -
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hwk
hwk is a tool used for wireless lan pentests
hwk is an easy-to-use application used to attack and discover wireless networks. It's providing various modes such as authentication/deauthentication flood, beacon and probe response fuzzing. -
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PhyloTreePruner
A nifty Java program for pruning phylogenetic trees.
...These trees are then provided to PhyloTreePruner which checks them for evidence of paralogy (i.e., multiple sequences from the same taxon that do not form a clade), trims suspected paralogs from the data matrix, and generates a new alignment containing only sequences inferred as orthologs. Preliminary tests of PhyloTreePruner on a variety of datasets indicate that this method successfully removes paralogous sequences and thus should help improve the accuracy of inferred species trees. -
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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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Hierachical_DNAcoder
An Hierachical Approach to Multi-Reference Genome compression
The storage and data transferring of large genome data are becoming important concerns for biomedical researchers. We present a novel multi-reference based genome compression method with a hierachical structure. Our approach works for the de facto standard alignment format (i.e., BAM) compression that is the pressing need at present. We align new sequences to a reference sequence using SOAP3, a GPU-based aligning software, and summarize mapping properties and information for exact mapped reads. To increase the exact aligning rate, we also realign the approximately mapped and unmapped reads by changing the reference sequence or shortening the read length. ... -
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Vanator-CVR
A metagenomics & virus discovery pipeline
Vanator (Virus Alignment, de Novo Assembly and Taxonomy On Reads) is a Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples. The philosophy behind Vanator is described by Jarrett et al (2013) http://www.ncbi.nlm.nih.gov/pubmed/23296970 -
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ProGraphMSA
Graph-based multiple sequence alignment
...Further, we account for variations in the substitution pattern by using estimated amino acid frequencies and by implementing context-specific profiles as in CS-Blast. The latest versions of ProGraphMSA include and extension to the alignment model to support tandem repeat unit insertions and deletions. -
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LaTeX Table Creator
Simple Cross-platform LaTeX table creator with a GUI and console app.
...Uses the output of standard spreadsheet software (MS Office, Libre Office, Gnumeric) to create a LaTeX tabular object that contains the specified data. Automatically detects the size of the table. The user can optionaly specify some basic formatting information, such as alignment, borders, bold headings. The user can also select if the input is tab (default) or comma delimited and can disable the tabular structure in the output. This allows the output to b easily appended to an existing table. This application is intended for importing "large" amounts of data into a LaTeX table. It is not intended to make fancy formatting easier. ... -
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Component for structural analysis (graph-based concept and entity linking, segmentation and alignment of comparable texts)
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ContigScape
Cytoscape plugin for visualizing contig relationships
ContigScape is a Cytoscape plugin which utilize ace and mate-paired alignment for visualizing the relationship between contigs.
