Search Results for "alignment" - Page 15
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Showing 522 open source projects for "alignment"
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PrintLogo
Free Joomla! plugin to display a header-logo on printed pages.
Free and simple Joomla! system-plugin to display an own header-logo on top of the first page when printing with Joomla!'s integrated function. Activate this plugin and select a logo from the imagelist (upload your own custom logo to the "images/" path). More detailed information about each parameter setting can be found in the popup help text of the plugin parameter settings pane of Joomla!s admin back-end. -
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S-Match
S-Match is a semantic matching framework.
...S-Match contains implementations of the semantic matching, minimal semantic matching and structure preserving semantic matching algorithms. S-Match applies as a solution in many fields, including: information integration, ontology evolution and alignment, peer-to-peer information sharing, digital libraries integration, web service composition, agent communication, and query answering on the web. S-Match is extendable to host new algorithms. -
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mirUtils
miRNA alignment quantitation based on miRBase annotations
...Starting from a miRBase-aligned BAM/SAM file, mirUtils reports counts and quality metrics for several taxonomy levels, including miRNA precursor hairpins, hairpin groups and families, mature miRNA loci, mature sequences, and genomic clusters, as well as per-hairpin-position alignment start and base coverage details. -
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Flocking Motion
Flocking motion simulator
...Environment constants and boid algorithms can be changed and reimplemented to experiment and understand the control of the whole flock. Don't be afraid, keep in mind the three rules: Separation, Alignment and Cohesion, and you'll get beautiful patterns in movement. -
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ALTER is a web-based tool to transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.
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Digital Expression on the Web
DEW is a platform that allows users to explore RNA-Seq data
...When provided with multiple isoforms and in the ‘contextual’ mode, corrections include a expectation maximization algorithm estimates effective expression profiles and a corrected alignment is produced. For each gene the user provides, DEW computes coverage descriptive statistics (RPKM, FKMP and total, mean and median corrected counts), expression profiles (normalized as R/FPKM and trimmed mean of fold change). DEW allows users to explore the data by providing interactive graphs. -
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SimplyTheBlast
Blast query sequences on a set of fasta formatted genomes
...This code requires: Bio::SeqIO; Bio::Perl; Bio::Tools::Run::StandAloneBlast; Bio::Seq; Bio::Tools::Blast; Bio::DB::GenBank; Bio::DB::WebDBSeqI; and BLAST 2.2.28 (blastall and formatcmd) installed and reachable from your command line Usage: perl SimplyTheBlast-Align.pl <fasta formatted seeds file> <path to genomes folder> <Alignment length threshold in %> <Alignment identity threshold in %> OR Usage: perl SimplyTheBlast-Evalue.pl <fasta formatted seeds file> <path to genomes folder> <Evalue threshold> Genomes files names must end with *.faa Output files: TABULAR_FBH_OUTPUT.xls is an Excel readable file with the identifier of the best hits found TABULAR_FBH_OUTPUT.csv is a file with the number of the best hits found query_n* files are fasta formatted files with the sequences of the best hits found bugs /comments: marco.fondi@unifi.it -
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Fast Alignment Search Tool suite. A fast sequence read mapper suite for short reads generated with the Illumina platform. Contains mrFAST and mrsFAST. Joint development by University of Washington and Simon Fraser University
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DNATweezer
A suite of BioPerl wrappers for manipulating DNA and protein sequences
...These scripts provide command-line access to the most frequently used BioPerl DNA object methods e.g. reverse-complement and translation of DNA sequences, slicing a sequence alignment, rerooting a phylogenetic tree, and calculating diversity of a population of DNA sequences. -
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dna-bison
Bisulfite alignment On Nodes of a cluster
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2. Multiple compute nodes are not absolutely required, but will make the alignment process faster. Further details available on the Wiki page. Help also available on SEQanswers (http://seqanswers.com/forums/showthread.php?t=31314) or by creating a ticket here. You can now track the development on github (https://github.com/dpryan79/bison). There is now a tutorial available in the downloads here: http://sourceforge.net/projects/dna-bison/files/bison_tutorial.tar.gz/download . -
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CUSHAW2: Parallel Gapped Read Alignment
One of the leading short-/long-read aligner to large genomes
CUSHAW2 is a fast and parallel gapped read alignment to large genomes, such as the human genome. The performance evaluation, by aligning simulated and real datasets to the human genome, shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed. Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads. -
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COV2HTML
A visualization and analysis tool of Bacterial NGS data for Biologists
COV2HTML provides an easy and 'in home' web interface for biologists that allows coverage visualization of the NGS alignment needed for the analysis. It combines two essential processes: (i) MAP2COV, a tool that converts the huge NGS mapping or coverage files into light specific coverage files which contains genetic elements informations. (ii) COV2HTML, a visualization interface allowing a real-time analysis of data with selected criteria. Thus this interface offers a visualization of NGS mapping coverage data (DNA-seq, RNA-seq, ChIP-seq and TSS) performed in different prokaryotic organisms (bacteria, viruses...) or different experimental conditions (mutant versus wild type strains or different growth states…) facilitating studies. -
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GBLASTN
G-BLASTN is a GPU-accelerated nucleotide alignment tool.
G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. G-BLASTN can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries. -
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jaivox
Speech recognition application builder and library
Java library and tools to create open source speech recognition applications. Generates dialogs for conversational interfaces. Works with a popular open source speech recognition library. -
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MetaDomain
Protein domain classification for short sequences
MetaDomain is a protein domain classification tool designed for very short next-generation sequencing reads. It achieves better sensitivity and low false positive rate compared with the state-of-the-art profile hidden Markov model (profile HMM) alignment tool in identifying encoded domains from short sequences. -
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MARAGAP
MARAGAP - Modular Approach to Reference Assisted Genome Assembly Pi...
...MARAGAP uses an algorithmic approach to detect and correct inversions and deletions, a De-Bruijn graph based approach to infer the insertions, an affine-match affine-gap local alignment tool to estimate the locations of those insertions and a Bayesian estimation framework for SNPs. -
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...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. Updates: FrameBot now uses a kmer pre-filtering heuristic for no-metric-search. This pre-filtering may increase the speed by one to two orders of magnitude. ...
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FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
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Seal
A toolkit for distributed processing of HT sequencing data.
Seal is a Hadoop-based distributed short read alignment and analysis toolkit. Currently Seal includes tools for: read demultiplexing, read alignment, duplicate read removal, sorting read mappings, and calculating statistics for empirical base quality recalibration. Seal scales, easily handling TB of data. -
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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. ... -
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Bycom
Bycom can do methylcytosine calling (5mC calling) from BS-seq.
...Several parameters in Bycom could be set as what the users want to, such as depth threshold, quality control value, conversion rate, processor number. 3. Bycom do the mapping based on BSMAP, and provide the parameters using in the alignment. -
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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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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Weather
Weather - Command Line Current & Recent
This one has a built-in Station ID Database and shows the last 24hr readings. It is easy to use, is only one file, and there is a version for 32bit Linux and 64bit Windows.
