BOL: Related items

Epiviz: an interactive visualization tool for functional genomics data.

Jit — Mon, 09 Jul 2018 05:27:39 -0500

Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can addd3 visualizations. You can see a video tour here.

https://bioconductor.org/packages/release/bioc/html/epivizr.html

https://github.com/epiviz

https://github.com/epiviz/epiviz

Address of the bookmark: https://epiviz.github.io/

visNetwork: an R package for network visualization, using vis.js javascript library

Jit — Wed, 09 Jan 2019 11:00:32 -0600

visNetwork is an R package for network visualization, using vis.js javascript library (http://visjs.org/). All remarks and bugs are welcome on github : https://github.com/datastorm-open/visNetwork.

Features

Based on htmlwidgets, so :

compatible with shiny, R Markdown documents, and RStudio viewer

The package proposes all the features available in vis.js API, and even more with special features for R :

easy to use
custom shapes, styles, colors, sizes, …
works smooth on any modern browser for up to a few thousand nodes and edges
interactivity controls (highlight, collapsed nodes, selection, zoom, physics, movement of nodes, tooltip, events, …)
visualize rpart tree

Address of the bookmark: https://datastorm-open.github.io/visNetwork/

Circos visualization !

BioStar — Mon, 06 Mar 2023 06:01:32 -0600

Circos visualization

https://wlcb.oit.uci.edu/modules/index.html

Address of the bookmark: https://wlcb.oit.uci.edu/NG-Circos

A web-based tool for sequence alignment statistics and innovative visualization

BioStar — Thu, 04 Apr 2024 01:44:50 -0500

AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/

Genome Annotation

Sun, 25 Aug 2013 10:53:01 -0500

Dr. Rob Edwards describes some of the problems, challenges, and approches in genome annotation, with a particular emphasis on how the Fellowship for the Interpretation of Genomes (FIG) developed subsystems using the SEED database available at http://www.theseed.org/

Centurion

Jit — Fri, 12 Feb 2016 04:45:41 -0600

Although centromeres are essential for life and are the subject of extensive research, centromere locations in yeast genomes are difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation assay Hi-C has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples, and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single yeast genome by exploiting the centromeres’ tendency to cluster in 3D space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use two metagenomic samples with relatively low coverage Hi-C data to infer centromere locations for each chromosome in 14 different yeast species. For yeasts with large centromeres (e.g., S. pombe) Centurion predicts the exact centromere locations. For seven yeasts with point centromeres, Centurion predicts most of the centromeres at an average of 5~kb distance from their known locations. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results suggest that Centurion can be used for centromere identification for a large number of yeast species, even with a limited amount of Hi-C sequencing.

Paper:http://www.ncbi.nlm.nih.gov/pubmed/25940625

More at http://cbio.ensmp.fr/centurion/

Address of the bookmark: http://cbio.ensmp.fr/centurion/

DIYA: a bacterial annotation pipeline for any genomics lab

Jit — Fri, 30 Jun 2017 08:48:26 -0500

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

http://gmod.org/wiki/Diya

Address of the bookmark: https://sourceforge.net/projects/diyg/

DRAM: Distilled and Refined Annotation of Metabolism

BioStar — Sat, 06 Jul 2024 04:19:45 -0500

DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs. DRAM annotates MAGs and viral contigs using KEGG (if provided by the user), UniRef90, PFAM, dbCAN, RefSeq viral, VOGDB and the MEROPS peptidase database as well as custom user databases. DRAM is run in two stages. First an annotation step to assign database identifiers to gene, and then a distill step to curate these annotations into useful functional categories. Additionally, viral contigs are further analyzed during to identify potential AMGs. This is done via assigning an auxiliary score and flags representing the confidence that a gene is both metabolic and viral.

Ref https://genomicsaotearoa.github.io/metagenomics_summer_school/day4/ex15_gene_annotation_part3/#overview-of-drampy-annotate-output

Address of the bookmark: https://github.com/WrightonLabCSU/DRAM

KOBAS: a web server for gene/protein functional annotation and functional gene set enrichment

Jit — Fri, 19 Oct 2018 09:36:11 -0500

KOBAS 3.0 is a web server for gene/protein functional annotation (Annotate module) and functional gene set enrichment(Enrichment module). For Annotate module, it accepts gene list as input, including IDs or sequences, and generates annotations for each gene based on multiple databases about pathways, diseases, and Gene Ontology. For Enrichment module, it can accept either gene list or gene expression data as input, and generates enriched gene sets, corresponding name, p-value or a probability of enrichment and enrichment score based on results of multiple methods.

Address of the bookmark: http://kobas.cbi.pku.edu.cn/

Detail annotation of genes !

Jit — Fri, 11 Jan 2019 05:23:33 -0600

gene_info recalculated daily
---------------------------------------------------------------------------
tab-delimited
one line per GeneID
Column header line is the first line in the file.
Note: subsets of gene_info are available in the DATA/GENE_INFO
directory (described later)
---------------------------------------------------------------------------

tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate

GeneID:
the unique identifier for a gene
ASN1: geneid

Symbol:
the default symbol for the gene
ASN1: gene->locus

LocusTag:
the LocusTag value
ASN1: gene->locus-tag

Synonyms:
bar-delimited set of unofficial symbols for the gene

dbXrefs:
bar-delimited set of identifiers in other databases
for this gene. The unit of the set is database:value.
Note that HGNC and MGI include 'HGNC' and 'MGI', respectively,
in the value part of their identifier. Consequently,
dbXrefs for these databases will appear like:
HGNC:HGNC:1100
This would be interpreted as database='HGNC', value='HGNC:1100'
Example for MGI:
MGI:MGI:104537
This would be interpreted as database='MGI', value='MGI:104537'

chromosome:
the chromosome on which this gene is placed.
for mitochondrial genomes, the value 'MT' is used.

map location:
the map location for this gene

description:
a descriptive name for this gene

type of gene:
the type assigned to the gene according to the list of options
provided in https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn

Symbol from nomenclature authority:
when not '-', indicates that this symbol is from a
a nomenclature authority

Full name from nomenclature authority:
when not '-', indicates that this full name is from a
a nomenclature authority

Nomenclature status:
when not '-', indicates the status of the name from the
nomenclature authority (O for official, I for interim)

Other designations:
pipe-delimited set of some alternate descriptions that
have been assigned to a GeneID
'-' indicates none is being reported.

Modification date:
the last date a gene record was updated, in YYYYMMDD format

Feature type:
pipe-delimited set of annotated features and their classes or
controlled vocabularies, displayed as feature_type:feature_class
or feature_type:controlled_vocabulary, when appropriate; derived
from select feature annotations on RefSeq(s) associated with the
GeneID

Address of the bookmark: ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/