Search Results for "loci"
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Showing 43 open source projects for "loci"
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BIGSdb
Software for storing and analysing bacterial sequence data
...Sequence data can range from single sequence reads to multiple contigs generated by whole genome sequencing technologies. The system incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into schemes for isolate characterisation or for evolutionary or functional analyses. See Jolley and Maiden 2010, BMC Bioinformatics 11:595 (http://www.biomedcentral.com/1471-2105/11/595). You can report bugs or make enhancement requests using the issues tracker at https://github.com/kjolley/BIGSdb. ... -
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Loci Framework
Autoparallelizing Framework for Scientific Modeling
The Loci framework provides an automatically parallelizing framework for numerical applications. Applications are represented as a database of rules and the framework generates schedules of rules to execute applications. -
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flowPsi
A compressible CFD flow modeling software package
The flowPsi code is a Loci framework code that provides a full featured open source solution to modeling compressible fluid flows. This software uses the Loci framework which can be found at https://sourceforge.net/projects/loci-framework -
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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GMATA software for Genomic SSR marker
Genome-wide Microsatellite Analyzing Toward Application: GMATA
What is software GMATA v21 Genome-wide Microsatellite Analyzing Toward Application (GMATA) is a software for Simple Sequence Repeats (SSR) analyses, and SSR marker designing and mapping in any DNA sequences. It has the following functions: 1. SSR mining; 2. Statistical analysis and plotting; 3. SSR loci graphic viewing; 4. Marker designing; 5. Electronic mapping and marker transferability investigation. GMATA is accurate, sensitive and fast. It was designed to process large genomic sequence data sets, especially large whole genome sequences. In theory, genomes of any size can be analyzed by GMATA easily. Software GMATA works on sever, desktop or even laptop, and it can run in graphic interface with just clicks or run in command line or in automated pipeline. ... -
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RGT
Repeat Genotyping Tool
...RGT identifies SSR structures from raw fastq reads, identifies and exports the gremlin alleles to the user, along with 2D plots of units counts (as electrophoresis plots). It also exports 3D plots of repeat units count vs each others in loci where there are more than one expanding repeat -
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GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is supported by the National Science Foundation (grant no. ... -
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ALDB
ALDB: a domestic-animal long noncoding RNA database
...ALDB currently comprises 12,103 pig lincRNAs, 8,923 chicken lincRNAs, and 8,250 cow lincRNAs, which we have identified using computational pipeline in this study. Moreover, ALDB provides related useful data, such as genome-wide expression profile and animal quantitative trait loci (QTLs), that is not available in the existing lncRNA database (lncRNAdb and NONCODE), along with convenient tools, such as BLAST, GBrowse and flexible search functionalities. Aimin Li, PhD School of Computer Science and Engineering, Xi'an University of Technology, 5 South Jinhua Road, Xi'an, Shaanxi 710048, P.R China liaiminmail AT gmail.com emanlee815 AT 163.com -
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...Applying this method on polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points, recognizing causal mutations in mutant genomes or QTL loci. In addition, inGAP-family provides user-friendly graphical interface for detection of polymorphisms and structural variants, and for further evaluation of predicted variants and identification of mutations related to genotypes. inGAP-family is implemented in Java to provide a platform-independent tool, and to support both command line mode and graphical mode. ...
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MeKin2D
Subroutines for planar mechanism simulation
MeKin2D is a collection of Free Pascal subroutines for kinematic simulation of planar linkage mechanisms using a modular approach. -
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Next-generation data pipeline to statistically call methylated and differentially methylated loci See the manual in doc/manual.pdf Please note: Calling of (differentially) methylated _positions_ will soon be uploaded.
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SUPERmerge
ChIP-seq coverage island analysis algorithm for broad histone marks
...SUPERmerge is especially useful for investigating low sample size ChIP-seq experiments in which epigenetic histone modifications (e.g., H3K9me1, H3K27me3) result in inherently broad peaks with a diffuse range of signal enrichment spanning multiple consecutive genomic loci and annotated features. -
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TrajectorEE
Trajectories of Loci during Experimental Evolution
Visualizes trajectories of loci during experimental evolution using forward simulations -
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PExFInS
Post-GWAS Explorer for Functional Indels and SNPs
The generation of Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) was originated from the observation that high proportion of cis-acting expression quantiative trait loci (cis-eQTLs) emerged in GWAS SNPs and the underexplored status of indel cis-eQTLs for GWAS. We believe that the integration of cis-eQTLs, especially indel cis-eQTLs, with candidate disease-associated variants generated from GWAS could facilitate the identification of causal genes or disease mechanisms. On the other hand, the biological information encoded in human genome, such as regulatory features from the Ensembl regulatory database, will be conductive in pinpointing functional causal variant(s) for the disease association. ... -
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The friendly GWAS SNP enrichment tool
Tests for enrichment of GWAS SNPs in epigenetic datasets
...The program will go through a directory of bed files e.g. all of the encode ChIP-seq datasets. Enrichment is checked against random samples from all the SNPs. The output is a tab delimited text file with the number of target loci hit, the mean number of background loci hit, the fold enrichment and a P value derived from the number of background permutations that hit as many or more loci as the test SNPs, divided by the number of permutations. -
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Simple GWAS catalogue pruner
Prune GWAS SNPs for a trait based on distance from each other.
...The user can select the distance. If two SNPs are within the user defined distance then the more proximal one on the chromosome will be discarded. This is a way of rapidly pruning a set of GWAS loci that are themselves in LD with each other. Avoids the complexities of basing the pruning on LD. -
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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. Extract files and run the jar file!
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Application to estimate haplotypes and other genetics data, based on maximum likehood approach. It can handle present-absent as well as multiallelic loci.
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...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. BMC Genomics 2014 15:858.
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jChIP
Graphical environment for exploratory ChIPSeq data analysis
jChIP is a GUI-based Java application for ChIP-Seq data analysis. It was created to build binding profiles between proteins and loci in the genome. In addition it computes statistics of the number of loci/positions containing specified amount of tags. jChIP is able to load data in several common formats (SAM, BAM, WIG, BED, Bowtie) and download loci definitions directly from the Ensembl database. http://www.biomedcentral.com/1756-0500/7/676 -
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RAREVATOR
Tool for the detection of variants in rare reference allele loci
RAREVATOR (RAre REference VAriant annotaTOR) is a tool for the identification and annotation of germline and somatic variants in rare reference allele loci from second generation sequencing data. RAREVATOR has been published on BMC Genomics. Magi A, D'Aurizio R, Palombo F, Cifola I, Tattini L, Semeraro R, Pippucci T, Giusti B, Romeo G, Abbate R, Gensini GF. Characterization and identification of hidden rare variants in the human genome. BMC Genomics. 2015 Apr 24;16:340. doi: 10.1186/s12864-015-1481-9. -
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2bRAD-denovo
THIS REPOSITORY HAS BEEN MOVED TO GITHUB
Download the latest updates from https://github.com/z0on/2bRAD_denovo 2bRAD is a method for cost-efficient whole-genome genotyping, described in Wang et al 2012 http://www.nature.com/nmeth/journal/v9/n8/abs/nmeth.2023.html This project is about analyzing 2bRAD data without a genome reference. Scripts and walkthroughs for: - trimming and quality filtering; - removing PCR duplicates; - assembling loci; - calling variants (SNP-wise and haplotype-wise); - recalibrating quality scores based on genotyping replicates; - smart-thinning and final filtering; - quality assessment based on replicates. Also included are walkthroughs for analysis: - computing Weir and Cockerham Fst - BayeScan - ADMIXTURE - fastSTRUCTURE -
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gametes
Generate complex SNP models and heterogeneous datasets
...GAMETES is designed to generate epistatic models which we refer to as pure and strict, that constitute the worst-case in terms of detecting disease associations, since such associations may only be observed if all n-loci are included in the disease model. User friendly GAMETES software rapidly and precisely generates epistatic multi-locus models, and can generate simulated datasets based on these models. Version 2.0, adds the ability to generate heterogeneous datasets by applying multiple independent models to different subsets of the simulated data. ... -
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CCH
A genetics tool that identifies genomic regions of shared ancestry
Combinatorial Conflicting Homozygosity (CCH) uses dense Single Nucleotide Polymorphism (SNP) genotypes to identify regions of the genome inherited from a common ancestor among any or all subsets of a group. Analysis is rapid and can identify loci containing genes for dominant traits. CCH is robust to the presence of phenocopies and can detect undisclosed shared common ancestry. The associated publication regarding CCH may be accessed here: http://www.biomedcentral.com/1471-2164/16/163 If you use CCH please cite: Levine AP, Connor TM, Oygar DD, Neild GH, Segal AW, Maxwell PH, Gale DP. ...
