Search Results for "multiple sequence alignment" - Page 7
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Showing 311 open source projects for "multiple sequence alignment"
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Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutit
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Protospacer Workbench
CRISPR/Cas9 guide-RNA design
Protospacer Workbench helps to design, analyze, and share CRISPR target-sites for any organism or set of FASTA formatted sequences. Design of guide-RNAs for the CRISPR/Cas genome editing system is intuitively easy, but computationally difficult. The main difficulty arises from the need to identify potential off-targets that may be quite different from the intended target. Current online tools for guide-RNA design provide a user friendly interface to sequence mapping software such as... -
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PROMOT
A tool for finding functional motifs from aligned protein sequences
PROMOT (version 4.0) is a bioinformatics tool for discovering motifs (in the PROSITE format) from a set of aligned 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 >... -
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This tool helps you to reverse engineer UML Sequence Diagram for your java program at runtime. It works well with both complex java programs (that have multiple threads) and J2EE applications deployed on Application Servers.
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Generic REST Fetcher
Execute a cascading sequence of REST calls to a common end-point
REST API's often require multiple calls to achieve a business objective. Eg get a list of objects, then get data for each object. This application allows you to transform data received from one REST call to determine other methods to call. All this is configured via an XML file. A simple example is fetching data for all respondents to a Survey Monkey survey. You need to get the set of respondent ids, then call the API passing in the list of respondent ids. See the README.md file on... -
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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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ASCOM driver for the LittleFoot Elegance Photo (LFEP) telescope controller. Firmware 6.x is fully supported - firmware 5.x is partially supported (all LFEP features are available but configuration is only possible by handbox). Contains drivers for telescope, focuser, camera, filter wheel, roof controller and dew heater which shares a single connection to the controller.
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Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
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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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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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REDHORSE
Software suite for the analysis of haploid hybrids using NGS
The alignments to the genome from next-generation-sequencing (NGS) data cannot be directly used as input to the existing recombination detection (RD) algorithms that use multiple sequence alignments (MSA). We therefore designed a software suite called REDHORSE that takes genomic alignments as input, extracts meaningful markers and generates MSAs that are the inputs to existing RD algorithms. In addition, REDHORSE implements a custom RD algorithm that makes use of sequence information and genomic positions to accurately detect crossovers. ... -
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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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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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...Both images with single spot groups and multiple spot groups (372 and 324 spots/group) can be processed. Example of such images were taken from the GEO and SMD databases. e.g., GSM102718 - GEO experiment for single spot group.
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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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NUCPOS
Suite for analysis of genome-wide nucleosome positions
NUCPOS is a suite of utilities for the analysis of genome-wide nucleosome positions. The suite is currently composed of 5 programs: nucfrag dyad_bins align_dyads dinucleotide_frequencies hp_fft The analysis starts with the SAM format alignment file generated by an alignment program such as Bowtie2. All utilities are coded in C++ 11, and can easily be modified to use any available genome sequence. -
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CEMAsuite
Consensus/Degenerate Primer Design Application
CEMAsuite, is an interactive Java-based application with the ability to (i) construct a codon-equivalent multiple alignment (CEMA) from a protein multiple sequence alignment (MSA) file, (ii) generate and score each position in the consensus DNA sequence using multiple algorithms, (iii) design single-degeneracy primer backbones using Primer3 (Untergasser et al. 2012), (iv) estimate the stability of degenerate primers on each of the coding sequences within the CEMA, and (v) export intermediate results in various formats. ... -
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LowMACA
Low frequency Mutation Analysis via Consensus Alignment
...However, we are still far from a complete picture of rarely mutated genes, which can be an important target for personalized medicine. To overcome this difficulty, we have implemented LowMACA (Low frequency Mutation Analysis via Consensus Alignment), a new method able to assess specific characteristics of rarely mutated genes that show patterns of positive selection. LowMACA aggregates and analyzes the mutational patterns of several genes whose encoded proteins have a high level of sequence similarity or share specific protein domains. -
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Matplotlib tutorial
Matplotlib tutorial for beginner
...As the tutorial builds progressively, learners can gradually advance from simple static plots to more complex visualizations, learning how to control figure size, add multiple subplots, adjust plot aesthetics, and handle different data types. Because it is code-first, users can copy, modify, and run the examples on their own datasets, encouraging experimentation and deepening understanding. -
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RT-alignment
Graph-based time alignment algorithms for multiple LC-MS datasets
...An LC-MS analysis of a complex biological sample can be visualized as a “map” of which the positional coordinates are the mass-to-charge ratio (m/z) and chromatographic retention time (RT) of the chemical species profiled. Label-free quantitative-proteomics requires the alignment and comparison of multiple LC-MS maps to ascertain the reproducibility of experiments or reveal proteome changes under different conditions. The main challenge in this task lies in correcting retention time shifts, which are inevitable even on the same instrument and under the same elution conditions. For large-scale studies, multiple instruments or multi-week experiments are often required, which exacerbates the problem. ... -
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AlignMerger
A tool for merging two large multiple sequence alignments
AlignMerger is useful to merge two sets of multiple sequence alignments (MSA). It can greatly reduce the computational time needed to construct a MSA, compare to others commonly used MSA tools. Inputs required for the tool are two MSAs in FASTA format and output of the tool is a merged MSA in FASTA format. -
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Maximum Common Genome Alignment (MCGA)
Pipeline for creating core genome alignments for phylogenetic analysis
Maximum Common Genome Alignment (MCGA) Tool MCGA is a bioinformatics analysis tool written in Python for generating core genome alignment for bacterial whole genome sequences which can be used to construct phylogenetic trees. -
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Editor.md
The open source embeddable online markdown editor (component)
The open source embeddable online markdown editor (component), based on CodeMirror & jQuery & Marked. The available dependents are CodeMirror, marked, jQuery, FontAwesome, github-markdown.css, KaTeX, prettify.js, Rephael.js, flowchart.js, sequence-diagram.js, and Prefixes.scss. You can enable HTML tags decode, TeX, Flowchart, sequence diagram, Emoji, FontAwesome, task lists. You can also enable image upload, [TOCM], search replace features, code fold, etc. Combine multiple JS module files used by CodeMirror to greatly reduce HTTP requests and speed up downloading. In addition, when using Require.js, because of CodeMirror's strict module dependency restrictions, the merged module files cannot be used, and multiple module files are still dynamically loaded. ... -
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SWAPHI-LS: Alignment on Xeon Phi Cluster
Smith-Waterman long DNA sequence alignment on Xeon Phi clusters
The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host. -
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Fast Alignment Search Tool suite. A fast sequence read mapper suite for short reads generated with the Illumina platform. Joint development by University of Washington and Simon Fraser University
