Search Results for "gene prediction"
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Showing 40 open source projects for "gene prediction"
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AlphaGenome
Programmatic access to the AlphaGenome model
...This repository contains client-side code, examples, and documentation to help you use the AlphaGenome API. AlphaGenome offers multimodal predictions, encompassing diverse functional outputs such as gene expression, splicing patterns, chromatin features, and contact maps. The model analyzes DNA sequences of up to 1 million base pairs in length and can deliver predictions at single-base-pair resolution for most outputs. AlphaGenome achieves state-of-the-art performance across a range of genomic prediction benchmarks, including numerous diverse variant effect prediction tasks. -
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FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013.
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CPAT
RNA coding potential assessment tool
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC , PhyloCSF and RNACode ). ... -
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University, see http://arthropods.eugenes.org/EvidentialGene/ Construction refers to the combination of classical gene prediction, and more recent gene assembly (de-novo and genome-assisted) methods. -
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miRPV
miRPV: An automated pipeline for miRNA Prediction and Validation in si
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence. System Requirement CPU: AMD64 (64bit) Memory: 2Gb RAM Storage: 5Gb Ubuntu 18.04 -
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chimera
ChiMera: An easy-to-use pipeline for Genome-based Metabolic Network re
There is a scarcity of user-friendly tools that can be used in daily routine, providing insights about the metabolic network of a target organism for researcher’s groups. Here we present a novel tool, Chimera, which combines the most efficient tools in model reconstruction, prediction, and visualization and also implements new in-house algorithms for database integration and data manipulation. Our goals: Produce an organism-specific model based on the CarveMe algorithm Manage the model and perform growth predictions with COBRApy Create visualization for the metabolic network using PSAMM and Escher Add pathway information to metabolic maps using in house algorithm Perform single and double, gene and reaction, knockout in the organism -
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CODON SOFTWARE
The dataset and codon project files are available here.
Genome annotation conceptually consists of inferring and assigning biological information to gene products. Over the years, numerous pipelines and computational tools have been developed aiming to automate this task and assist researchers in gaining knowledge about target genes of study. However, even with these technological advances, manual annotation or manual curation is necessary. To assist with this problem, we present CODON, a tool for the prediction, annotation, and manual curation of genomic data. ... -
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Fun4Me
A package for functional annotation for metagenomes
This package includes a few programs for rapid functional annotation for metagenomic sequences, including, 1) Gene prediction by FragGeneScan; 2) Similarity search by RAPSearch2; 3) Functional annotation in GO (Gene Ontology) and EC (Enzyme Commission) based on similarity search results; 4) From EC to metabolic pathway reconstruction by MinPath. Inputs: Just sequencing reads (or assemblies) Outputs: Protein-coding genes (or gene fragments); similarity search; functional annotations (in GO and EC); metabolic pathways. -
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Microarray assosiated motif analyzer
Cis-element prediction tool from microarray data
We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. After optimization, MAMA accurately simulated more than 87% of gene expression. ... -
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The GeneRFinder-Benchmark is a comprehensive benchmark data for gene prediction which is based on data of CAMI (Critical Assessment of Metagenome Interpretation) and contains labeled data from gene regions. The benchmark is made up of 9 datasets. For each one of them is provided: - List of names, taxonomy ID and taxonomic level of the genomes of the organisms that make up the dataset (genomes.csv) - Set of sequences extracted from the respective selected genomes (sequences.fasta) - Ground truth for each of the extracted ORFs (groundtruth.csv) For information about download, see the documentation.
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SpliceGrapher predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene's exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.
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altanalyze
Alternative splicing and functional prediction analysis tool
AltAnalyze is a freely available, open-source and cross-platform program that allows you to take RNASeq or relatively raw microarray data (CEL files or normalized), identify predicted alternative splicing or alternative promoter changes and view how these changes may affect protein sequence, domain composition, and microRNA targeting. AltAnalyze is compatible with any RNASeq data (exons and/or junctions), several Affymetrix splicing sensitive array types (Gene 1.0, Exon 1.0, junction) as... -
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OncoBase
A platform for decoding regulatory somatic mutations in human cancers
Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers. The vast majority of identified somatic mutations are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput chromosome conformation capture (3C)-based technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements... -
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GPRED-GC
a Gene PREDiction model accounting for 5'-3' GC gradient
A new hidden Markov model (HMM)-based ab initio gene prediction tool for finding genes with highly variable GC contents such as the genes with negative GC gradients in grass genomes. -
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DACO-algorithm
A novel transcription factor complex prediction algorithm.
Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. We developed DACO (domain-aware cohesiveness optimization), a novel algorithm that combines... -
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The Deep Review
A collaboratively written review paper on deep learning, genomics, etc
This repository is home to the Deep Review, a review article on deep learning in precision medicine. The Deep Review is collaboratively written on GitHub using a tool called Manubot (see below). The project operates on an open contribution model, welcoming contributions from anyone. To see what's incoming, check the open pull requests. For project discussion and planning see the Issues. As of writing, we are aiming to publish an update of the deep review. We will continue to make project... -
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wgssat_nbfgr
WGSSAT: SSR Annotation Pipeline
WGSSAT provides a Graphical User Interface pipeline to mine and characterize SSR from Whole genome data. This pipeline integrates prediction of genes, ncRNA, repeats and SSR from whole genome assembly and mapping of these predicted SSR on to the genome (classified according to genes, ncRNA, repeats, exonic and intronic region) along with primer designing and mining of cross-species amplification markers. The mining of SSRs from whole genome provides valuable information on the abundance of... -
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OncoIMPACT
Cancer driver prediction via integrative omics
OncoIMPACT is a model-driven approach to integrate omics profiles (genomics, transcriptomics etc.) and provides patient-specific cancer driver gene predictions. -
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Seqping
Gene Prediction Pipeline for Plant Genomes
Gene Prediction Pipeline for Plant Genomes using Self-Training Gene Models and Transcriptomic Data -
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SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
SnowyOwl is a gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions, and to evaluate the resulting models. The pipeline has been validated and streamlined by comparing its predictions to manually curated gene models in three fungal genomes, and its results show substantial increases in sensitivity and selectivity over previous gene predictions. -
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ConsPred
ConsPred is a pipeline combining several gene/CDS annotation tools
...Important notice: Conspred development has been ended with version 1.33 (except minor bug fixes). We are currently developing a completely rewritten Conspred2, which focuses on consensus gene prediction and high-quality gene start prediction. Conspred2 will not do any functional annotation (consider e.g. Prokka and GAMOLA2 for this purpose). -
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ingap-cdg
codon-based de Bruijn graph algorithm for gene construction
Currently, most gene prediction methods detect coding sequences (CDSs) from transcriptome assembly when lacking of closely related reference genomes. However, these methods are of limited application due to highly fragmented transcripts and extensive assembly errors, which may lead to redundant or false CDS predictions. Here we present a novel algorithm, inGAP-CDG, for effective construction of full-length and non-redundant CDSs from unassembled transcriptomes. inGAP-CDG achieves this by combining a newly developed codon-based de bruijn graph to simplify the assembly process and a machine learning based approach to filter false positives. ... -
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
miRNA is a widely known small non-coding RNA which can mediate gene regulation of most important biological processes in plants and animals. Therefore, identification conserve and novel miRNA and their target genes in model and new sequenced species are inevitable. MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result).... -
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Genix: Bacterial Genome Annotation Pipel
A automated annotation pipeline for bacteria / archea genomes
Genix is an online automated pipeline for bacterial genome annotation that integrates the programs Prodigal, BLAST, RNAmmer, tRNAscan-SE, INFERNAL, ARAGORN and HMMER, and the databases Uniprot, Antifam and Rfam. -
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SILA
Automated bacterial and archaeal genome annotation system
SILA is a system for automated annotation of bacterial and archaeal genomes. It provides accurate gene prediction using a combination of tools (Prodigal and HGF) and a web site for task management and visualization of annotation. This project is in alpha stage. Please use the online service available at: http://www.bioinfo.ufpr.br/SILA/login.jsp Documentation (portuguese only): http://hdl.handle.net/1884/34801
