Search Results for "genes"
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Showing 169 open source projects for "genes"
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rafah
Random Forest Assignment of Hosts
One fundamental question when trying to describe viruses of Bacteria and Archaea is: Which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), which outperformed other methods for virus-host prediction. Our rationale was that the machine could learn the associations between genes and hosts much more efficiently than a human, while also using the information contained in the hypothetical proteins. Random forest... -
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popoolation
estimate natural variation and positive selection
PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation allows to calculate Tajima’s Pi, Watterson’s Theta and Tajima’s D with a sliding window approach for chromosomes or for set of genes. One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. We believe that PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. Documentation: https... -
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
... and assembly software, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate and score gene constructions. Over-produced constructions are classified by gene evidence for best qualities per "locus", including genome-aligned and gene-transcript aligned (genome-free) locus identification. All software developed for EvidentialGene is publicly available. See project wiki/blog for notes. -
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ARES
Antibiotic Resistance Evolution Simulator
ARES (Antibiotic Resistance Evolution Simulator) is a membrane computing-based model, able to simulate complex biological landscapes. It uses a nested membrane-surroundings entitites scheme formatted in a XML file. The created scenarios emulate entities as: i) Resistance genes, able to detoxify antibiotics. These genes can be located in the plasmid, in conjugative elements or in the chromosome; ii) plasmids and conjugative elements transferring genes between bacterial cells; iii) bacterial... -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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Article has been accepted for publication by the journal, "genes". To view the article, please go to MDPI website; please copy and paste the link "https://www.mdpi.com/2073-4425/14/7/1476/pdf" in web address area. If download is not automatically started, please go to the website by copy and paste the link "https://www.preprints.org/manuscript/202306.0366/v1". And click "peer-reviewed article".
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TransMCL
a noval Transcriptome optimization tool
To improve the quality of transcriptome assembly, we introduce TransMCL, a novel transcriptome optimization tool, to reconstruct full-length coding sequences while eliminating redundancy from assembled transcriptomes. TransMCL employs homologs from closely related species to guide the assembly, clustering raw transcripts from transcriptome data and genes from annotated genomes into hierarchical ortholog groups (HOGs). -
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In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing events. In so doing, it is feasible to compare two samples and identify genes with most significant difference in exon(splicing)-level.
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In addition to computing co-expression clusters, Maccu fishes potential co-expressed genes for a given bait set. All results can be further processed via graph-level operations so that we can compare graphs based on different reference data.
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... residues (e.g. Leu-, SR-, PEST-rich motifs, etc.), (ii) searches for multiple pre-defined consensus patterns or experimentally validated functional motifs in large datasets protein sequences (proteome-wide), (iii) map UniProt and PROSITE flat files. ShettiMotif can parse large dataset of sequences efficiently. Article: Haitham Sobhy; A bioinformatics pipeline to search functional motifs within whole proteome data; poxviruses a case study; Virus Genes, 2017; doi: 10.1007/s11262-016-1416-9; PMID:
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genppi
GENPPI: standalone software for creating protein interaction networks
Our software GENPPI is efficient because, for example, it creates interaction networks from the central genome of 50 species/lineages of Corynebacterium, with an average size of 2200 genes, in less than 40 minutes, on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships between species and obtained in Average Nucleotide Identity (ANI) analyzes. Also, It allows the user to define how he intends to explore the PP... -
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RIFTT
Robust identification of fusion genes in tumor transcriptomes.
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QUAST
Quality Assessment Tool for Genome Assemblies
QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. QUAST computes a number of well-known metrics, including contig accuracy, number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and in the manual). A comprehensive analysis results in summary tables (in plain text, tab-separated and LaTeX formats) and colorful plots. The tool also produces web-based reports condensing all information in one... -
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TabS7
Tab. S7 for CVP method
Tab. S7: List of driver genes found by the nine algorithms(Dendrix,MDPFinder,MEMo,CoMDP,e-Driver,OncoDriveCLUST,SCS,ExInAtor,CVP) in the eight datasets(GBM,CESC,PRAD,LUSC,OV,SARC,KIRP,LIHC). -
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Peptide Pattern Recognition
Software for non-alignment based analysis of DNA and protein sequences
...). Several genes encoding enzymes with the same activity are necessary for aerobic fungal degradation of cellulose in nature. PLoS One, 9, e114138. -
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PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative...
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. We thank the support from... -
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MutaNET
NGS Pipeline and Automated Mutation Analysis
MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance. -
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Allelome.PRO
A pipeline to define allele-specific genomic features
... expression to give a complete picture of the “allelome” by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased biallelic or noninformative. Allelome.PRO offers increased sensitivity to analyse lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. -
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Damage-Net
Program for meta-analysis of large-scale datasets into DNA-repair.
Welcome to Damage-Net! This page is no longer in use, please go to our very own website from now on! www.damage-net.co.uk Our websites has all the latest info, downloads and updates. -
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ChIP-BIT2
ChIP-BIT2 detects weak binding sites of TFs or HMs.
... for detecting narrow peaks in promoter regions as described in the following paper: Xi Chen et al., "ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles", Nucleic Acids Res (2016) 44 (7): e65. -
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... biopsy from cancers, quantitative transcriptome analysis to estimate accurate expression levels of genes or transcripts, and even single-cell sequencing of large cell populations. Operating system: Linux Programming language: C++ License: Non-Commercial Research Use Only
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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... -
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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... -
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miRDiana
MATLAB package to find the miRNAs targeting a list of genes
To select miRNA target genes we developed software in MATLAB® (MathWorks®) called miRDiana that collects the union of mouse validated targets from the TargetScan, MicroCosm, mirTarBase and miRWalk 2.0 databases. Firstly, the software downloads each database and preprocesses by standardizing the miRNA and gene names. It strips the miRNA names from the species ids and converts the gene names to the official symbols of the National Center for Biotechnology Information (NCBI) database. Next...