Search Results for "gene" - Page 2
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Showing 53 open source projects for "gene"
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SAT-Assembler
Scalable and accurate targeted gene assembly for large-scale NGS data
SAT-Assembler is a scalable and accurate gene assembly tool for large-scale RNA-Seq and metagenomic data. It recovers genes from gene families of particular interest to biologists with high coverage, low chimera rate, and extremely low memory usage compared with exiting gene assembly tools. Moreover, it is naturally compatible with parallel computing platforms. -
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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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miRStat
identification of common sets of microRNAs for groups of genes
miRStat enables identification of regulatory microRNA targeting several genes in a custom gene group. This Python application is based on the TargetScan 6.2 microRNA target prediction data. Conserved and Nonconserved site context+ scores files are required (unzip and place to directory with program). Available at http://targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61 -
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mitoMaker
mitoMaker - a mitochondria assembly and annotation script
...General pipeline: 1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches a target mitochondrial genome given. 2-searches for all mitochondrial gene features and circularization. 3-stores the best result found. 4-uses the best assembly as backbone for a reference based assembly, using MIRA and MITObim, trying to extend the mitogenome and close gaps. 5-annotates the best assembly, identifying the start and end position of each and every feature. 6-creates a folder with all the results (PNG, GENBANK, FASTA, SEQUIN, CAF, MAF and a stats logfile). -
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...IMPACT utilizes multi-reads in calling peaks and provides users with high-confidence peaks. In addition, IMPACT provides a completely integrated pipeline which produces downstream analysis results such as motif discovery and peak-to-gene annotation.
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Protospacer
Rapid gRNA design and validation for CRISPR
...Each Protospacer database is a simple catalogue of all possible Cas9 target-sites within a given FASTA sequence, i.e. all NGG/NAG sites. Protospacer then allows the user to sub-select targets from the database by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. From here, users are able to evaluate potential off targeting, to export results in FASTA format or tabulated (e.g. for Microsoft Excel), and to connect to the Integrative Genomics Viewer (IGVref) and view target-sites in the context of genomic annotations, amino acid translations, and HT-Seq data (for off-target validation). ... -
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SeqSelector
Tools to select sequences for capture enrichment of next-gen libraries
...The scripts require no knowledge of programming, and can be applied to genome sequences of model or non-model species. We suggest a workflow in which genes of interest are first identified from previous studies and publicly available datasets of functional gene annotation. Once a list of candidate genes has been identified, their sequences are selected from the reference genome. These sequences are used as a query during a BLAST search of the unannotated genome of a non-model species, and then the corresponding sequences are returned, which can be used to design baits for hybridization-based sequence capture. -
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CDPOPgui
GUI Frontend for CDPOP
CDPOPgui is a GUI Frontend for CDPOP What is CDPOP? CDPOP (Cost Distance POPulations) is a spatially-explicit simulator of gene-flow in complex landscapes to explain observed population responses and provide a foundation for landscape genetics. The program implements individual-based population modeling with Mendelian inheritance on a resistant landscape. Simulation begins with an initial homogeneous population and followed by divergence through time as functions of individual based movement, breeding and dispersal on a continuous cost surface. ... -
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srst
Short Read Sequence Typing
Update - SRST2 Now Available ------ 25 Sep, 2013 This project has now been replaced by SRST2 - Short Read Sequence Typing for Bacterial Pathogens, available at http://katholt.github.io/srst2/ The new SRST2 program does gene typing as well as MLST (e.g. typing resistance genes, virulence genes, etc). SRST2 is faster and more accurate than the old SRST, using bowtie2 to achieve local alignments (no need for flanking sequences) and a brand new scoring system. -
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ScreenSifter
ScreenSifter is a unique tool for RNAi Screen analysis and management
...ScreenSifter, to perform the sequential, user friendly, guided, and advanced statistical analyses of RNAi screening results. User can upload their raw signal intensities and will avail complete quality control of screen, hit selection, plotting of hit genes with gene ontology, comparing of replicates or comparing of channels. In addition, ScreenSifter has visualization tools to plot specific genes or gene groups in the screen data. ScreenSifter also provides Gene Set Enrichment Analysis (GSEA), protein-protein interaction directly on the plot. Publication: ScreenSifter: analysis and visualization of RNAi screening data Pankaj Kumar, Germaine Goh, Sarawut Wongphayak, Dimitri Moreau and Frédéric Bard BMC Bioinformatics. 2013 Oct 3;14(1):290. ... -
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Webapp
A web interface to the SnowyOwl gene prediction pipeline
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. -
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AMBIENT
Find active modules in metabolic networks using high-throughput data
...For example, scores for reactions based on transcriptional data of their annotated encoding genes can be used in the network and modules of coordinated expression changes can be found. This provides an alternative to pathway/gene set enrichment analyses which is simultaneously more flexible and more specific. -
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Application to create 'electronic fluorescent pictographic' representations of gene expression patterns. Created at the Provart lab of the department of Cell & Systems Biology, University of Toronto.
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Python library to extract EXIF data from tiff and jpeg files. Very easy to use - $ ./EXIF.py image.jpg. Originally written by Gene Cash / Thierry Bousch. Fork of https://sourceforge.net/projects/exif-py/ Ported to Python 3 by Kayo.
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Hoea is a python module for hierarchical ontology enrichment analysis, which facilitated GO (Gene Ontology)/KO (KEGG Orthology) enrichment analysis at any desktop.
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Reliability Oriented Bioinformatic Networks Visualization
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At the outset, the goal of this program is to provide a suite of tools to aid in the back-translation of amino acid sequences in a manner that provides useful information for synthetic gene design.
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This is a multi-select tree widget for tkinter for python. This is an extension of Gene Cash's Tkinter tree widget (available from http://home.cfl.rr.com/genecash/) which works with python 2.5 as well as Python 3k.
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go2Sim measures semantic similarity between genes annotated with Gene Ontology terms. Resnik and Wang methods supported. A new improvement of the methods is currently in development, it will be available as soon as the results have been published.
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Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.
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SeqFreed is a bioinformatics desktop. It provides efficient access to sequence data and gene features, a customizable command line interface to locally installed bioinformatic tools and flexible display of either text or images in different page modes.
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QTL Reaper analyzes data from progeny of a genetic cross in experimental plants or animals. It seeks the location of genes that affect a heritable trait, and it is specially designed for analysis of gene expression measurements.