BOL: Related items

Flanker

Rahul Nayak — Sat, 27 Feb 2021 22:04:53 -0600

Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.

Address of the bookmark: https://github.com/wtmatlock/flanker

GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes

Abhi — Tue, 28 Dec 2021 01:49:03 -0600

A phylogeny based comparative genomics software to analyze the genetic environment of genes. The user can select one or several taxa and provide one or several reference protein(s). Genomes and plasmids (based on user choice) will be downloaded from the NCBI Assembly/NR database and searched for the respective gene. Alternatively, custom genomes can be provided. User selected stretches (20kbp by default) of the genes genetic environment are extracted, annotated and aligned between all genomes. The sequences are then visualized, enabling comparison of synteny and gene content.

More at https://pubmed.ncbi.nlm.nih.gov/34951622/

Address of the bookmark: https://github.com/EbmeyerSt/GEnView

2.4 Mb Genome Size for World's Biggest Virus

Jitendra Narayan — Thu, 08 Aug 2013 10:05:37 -0500

The genome size of new discovered Pandoraviruses have roughly twice the size of the record-holding Megavirus genomic code. Interestingly only 6 percent of its genes resembled the genes other organisms. It is assume that it may come from a different origin.

For detail : http://www.sciencemag.org/content/341/6143/281

http://www.npr.org/blogs/health/2013/07/18/203298244/worlds-biggest-virus-may-have-ancient-roots

RCircos: an R package for Circos 2D track plots

Jit — Fri, 20 May 2016 11:01:13 -0500

RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

BRAKER: pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

Jit — Thu, 01 Sep 2016 08:02:59 -0500

Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction.

http://www.ncbi.nlm.nih.gov/pubmed/26559507

Address of the bookmark: http://bioinf.uni-greifswald.de/bioinf/braker/

Enrichr: a comprehensive gene set enrichment analysis

Jit — Thu, 27 Apr 2017 05:42:09 -0500

Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw377

Address of the bookmark: http://amp.pharm.mssm.edu/Enrichr/

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/

BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly

Jit — Mon, 22 May 2017 05:43:51 -0500

This tool is for users to upgrade their metagenomics assemblies using long reads. This includes fixing mis-assemblies and scaffolding/gap-filling. If you encounter any issues, please contact me at kklam@eecs.berkeley.edu. My name is Ka-Kit Lam.

https://github.com/kakitone/MetaFinisherSC

https://github.com/kakitone/BIGMAC

Address of the bookmark: https://github.com/kakitone/BIGMAC

Hapsembler: An Assembler for Highly Polymorphic Genomes

Jit — Tue, 22 May 2018 04:09:53 -0500

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. http://compbio.cs.toronto.edu/hapsembler/

Address of the bookmark: http://compbio.cs.toronto.edu/hapsembler/

P10K: The Protist 10,000 Genomes

BioStar — Sat, 06 Jul 2024 08:29:30 -0500

The Protist 10,000 Genomes (P10K) Project aims to decipher the genome sequences and construct a comprehensive database resource containing over 10,000 species of protists, encompassing representatives from every major clade. Samples were collected from diverse habitats, and the genome information was acquired through de novo sequencing, genome re-annotation, and integration of publicly available data. Serving as a centralized data portal for the project, the P10K database primarily focuses on delivering high-quality curation and facilitating efficient retrieval of protist genome data.

Address of the bookmark: https://ngdc.cncb.ac.cn/p10k/