BOL: Related items

Mercator: Multiple Whole-Genome Orthology Map Construction

Jit — Tue, 19 May 2020 16:46:22 -0500

Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an ancestral genome. However, it has been pointed out that this use of the term is incorrect (Passarge et al. 1999) and thus we will use the terms "homologous", "orthologous", and "paralogous" instead. Ideally, given K genomes, we would like to identify all orthologous genomic regions as well as paralogous regions within each genome and hypothetical ancestral genome. Maps listing these relationships are extremely valuable to researchers performing comparative analyses of genomic sequence. Here we present our initial work in the form a program called Mercator that constructs orthology maps between multiple whole genomes.

Address of the bookmark: https://www.biostat.wisc.edu/~cdewey/mercator/

Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

Jit — Mon, 17 Feb 2020 05:38:46 -0600

Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assembled according to the genetic map, and split those scaffolds.

Address of the bookmark: http://catchenlab.life.illinois.edu/chromonomer/

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

LEGE — Mon, 06 May 2024 06:21:10 -0500

Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth http://synorth.genereg.net/ is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745767/

Address of the bookmark: http://synorth.genereg.net/

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/

chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes

Neel — Fri, 12 Apr 2019 05:30:41 -0500

Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R 'Shiny' applications.

Address of the bookmark: https://cran.r-project.org/web/packages/chromoMap/vignettes/chromoMap.html

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/

EUKulele: Taxonomic annotation of the unsung eukaryotic microbes

Shruti Paniwala — Sat, 26 Dec 2020 12:10:17 -0600

EUKulele, an open-source software tool designed to assign taxonomy to microeukaryotes detected in meta-omic samples, and complement analysis approaches in other domains by accommodating assembly output and providing concrete metrics reporting the taxonomic completeness of each sample.

Address of the bookmark: https://github.com/AlexanderLabWHOI/EUKulele