BOL: Related items

funannotate: Eukaryotic Genome Annotation Pipeline

Jit — Wed, 19 Sep 2018 07:47:22 -0500

Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this software package was to be able to accurately and easily annotate a genome for submission to NCBI GenBank. Existing tools (such as Maker) require significant manually editing to comply with GenBank submission rules, thus funannotate is aimed at simplifying the genome submission process.

Address of the bookmark: https://github.com/nextgenusfs/funannotate

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

Jit — Sat, 07 Sep 2019 10:45:31 -0500

chromoMap provides interactive, configurable and elegant graphics visualization of chromosomes or chromosomal regions allowing users to map chromosome elements (like genes,SNPs etc.) on the chromosome plot.Each chromosome is composed of loci(representing a specific range determined based on chromosome length) that, on hover, shows details about the annotations in that locus range. The plots can be saved as HTML documents that can be shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

Some of the prominent features of the package are:

visualizing polyploidy simultaneously on the same plot.
annotating groups of elements as distinct colors.
creating chromosome heatmaps.
adjusting chromosome range or visualizing chromosome regions such as genes
adding labels to the plot
adding hyperlinks to each element

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

Web Apollo: a web-based genomic annotation editing platform

Jit — Fri, 28 Jul 2017 04:48:17 -0500

Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.

Address of the bookmark: http://genomearchitect.github.io/

bpRNA: large-scale automated annotation and analysis of RNA secondary structure

Rahul Nayak — Wed, 23 May 2018 03:24:33 -0500

bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature.

The bpRNA code is written in perl and requires the Graph perl module. Several additional scripts for analysis are included. The source code is available at http://github.com/hendrixlab/bpRNA.

Address of the bookmark: http://github.com/hendrixlab/bpRNA

KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation

Abhimanyu Singh — Wed, 12 Dec 2018 09:16:55 -0600

KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data by BLAST and GHOSTX searches, respectively, against a nonredundant set of KEGG GENES. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to the BlastKOALA server and can be executed in an interactive mode. See Step-by-step Instructions.

Reference: Kanehisa, M., Sato, Y., and Morishima, K. (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731. [pubmed] [pdf]

Address of the bookmark: https://www.kegg.jp/blastkoala/

Apollo: First instantaneous, collaborative genomic annotation editor available on the Web

Jit — Fri, 31 May 2019 19:55:39 -0500

Apollo is a plug-in for the JBrowse Genome Viewer.
In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own configuration of the ‘Information Editor’.
History tracking with undo/redo functions is available.
Users are able to directly set an annotation to a specific state, choosing from the ‘History’ display.
Adding and updating PubMed IDs will prompt users with a publication title to confirm their submission.
Gene Ontology (GO) terms are supported and GO ID auto-completion has been incorporated.
Users may access a ‘Recent Changes’ page.
Help page with Apollo specific content is available.

Address of the bookmark: http://genomearchitect.github.io/

JCVI:Python utility libraries on genome assembly, annotation and comparative genomics

Jit — Tue, 17 Mar 2020 06:19:06 -0500

Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

https://github.com/tanghaibao/jcvi

More at https://github.com/tanghaibao/jcvi/wiki

Address of the bookmark: https://github.com/tanghaibao/jcvi

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

Jit — Wed, 13 Jan 2021 19:29:32 -0600

MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. Metaeuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to recover optimal exons sets. It reduces redundancies in multiple discoveries of the same gene and resolves conflicting gene predictions on the same strand. MetaEuk is GPL-licensed open source software that is implemented in C++ and available for Linux and macOS. The software is designed to run on multiple cores.

Address of the bookmark: https://github.com/soedinglab/metaeuk

CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation

Shruti Paniwala — Thu, 26 May 2022 00:59:49 -0500

CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall.

Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It should work on OSX, but please report any errors to maarten.reijnders@unil.ch or create an issue.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010075

Address of the bookmark: https://gitlab.com/mreijnders/crowdgo

PheWAS: R package is designed to provide an accessible interface to the phenome wide association study

BioStar — Thu, 30 Jul 2020 22:06:37 -0500

The PheWAS R package is designed to provide an accessible interface to the phenome wide association study. For a description of the methods available and some simple examples, please see the package vignette or the R documentation. For installation help, see below. ##Installing the PheWAS Package The PheWAS package can be installed using the devtools package. The following code when executed in R will get you started:

install.packages("devtools")
#It may be necessary to install required as not all package dependencies are installed by devtools:
install.packages(c("dplyr","tidyr","ggplot2","MASS","meta","ggrepel","DT"))
devtools::install_github("PheWAS/PheWAS")
library(PheWAS)

Address of the bookmark: https://github.com/PheWAS/PheWAS