BOL: Related items

Complete genome sequence of Wuhan seafood market pneumonia virus is out !

Jit — Fri, 31 Jan 2020 02:36:59 -0600

Wuhan-Hu-1 claimed at least 40 lives and infected at least 1300 others in China. Cases are now being reported from Thailand, Singapore, Malaysia, South Korea, Japan, Vietnam, Nepal, France, Australia and even as far as the US. On Jan 10 2020, while news of the first fatality was barely trickling in, the 29,903 letters constituting the viral genome from an affected individual in Wuhan had already been elucidated (even though a few corrections were made subsequently). All the viral genome sequences from affected individuals are very very close to each other. Several are identical and none has more than 5 differences (99.983% similarity). This strongly suggests that transmission into humans came from a single pointed source and happened very recently, between Sep-Dec 2019.

Check out the detail at https://www.ncbi.nlm.nih.gov/nuccore/MN908947

China’s BGI says it can sequence a genome for just $100

Neel — Sat, 29 Feb 2020 04:49:43 -0600

Using technology originally acquired in the US, the Chinese gene giant BGI Group says it will make genome sequencing cheaper than ever, breaking the $100 barrier for the first time.

The Shenzhen company says the low cost will be possible with an “extreme” DNA sequencing system it plans to offer that is capable of decoding the genomes of 100,000 people a year.

Ref: https://www.technologyreview.com/s/615289/china-bgi-100-dollar-genome/

Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome

BioStar — Wed, 22 Jul 2020 10:11:13 -0500

We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.

More at https://pubmed.ncbi.nlm.nih.gov/20494974/

Address of the bookmark: http://www.sequenceontology.org/cgi-bin/soba.cgi

Ancient whole genome duplication (WGD) detection tools !

Rahul Nayak — Sun, 07 Mar 2021 00:32:44 -0600

There are two methods for ancient WGD detection, one is collinearity analysis, and the other is based on the Ks distribution map. Among them, Ks is defined as the average number of synonymous substitutions at each synonymous site, and there is also a Ka corresponding to it, which refers to the average number of non-synonymous substitutions at each non-synonymous site.

At present, some people have posted articles about the analysis process of WGD. I searched for the keyword "wgd pipeline" and found the following:

GenoDup: https:// github.com/MaoYafei/GenoDup-Pipeline
https://peerj.com/articles/6303/
WGDdetector: https:// github.com/yongzhiyang2 012/WGDdetector
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2670-3
wgd: https:// github.com/arzwa/wgd
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1142-2#Sec1
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0399-x
GeNoGAP https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1142-2
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0399-x
https://github.com/dfguan/purge_dups
https://www.biorxiv.org/content/10.1101/2020.01.24.917997v1

This article introduces the usage of wgd.

Wgd cannot be installed directly with bioconda at present, so it is a little troublesome to install, because it depends on a lot of software. wgd depends on the following software

BLAST
MCL
MUSCLE/MAFFT/PRANK
PAML
PhyML/FastTree
i-ADHoRe

But the good news is that most of the software it depends on can be installed with bioconda

conda create -n wgd python=3.5 blast mcl muscle mafft prank paml fasttree cmake libpng mpi=1.0=mpich
conda activate wgd

Here mpi=1.0=mpich is selected, because i-adhore depends on mpich. If openmpi is installed, an error will appear while loading shared libraries: libmpi_cxx.so.40: cannot open shared object file: No such file or directory

After that, the installation is much simpler

git clone https://github.com/arzwa/wgd.git
cd wgd
pip install .
pip install git+https://github.com/arzwa/wgd.git
For i-ADHoRe, you need to register at http:// bioinformatics.psb.ugent.be /webtools/i-adhore/licensing/Agree to the license to download i-ADHoRe-3.0

Since my miniconda3 installed ~/opt/, the installation path is so~/opt/miniconda3/envs/wgd/

tar -zxvf i-adhore-3.0.01.tar.gz
cd i-adhore-3.0.01
mkdir -p build && cd build
cmake .. -DCMAKE_INSTALL_PREFIX=~/opt/miniconda3/envs/wgd/
make -j 4
make insatall

Take the sugarcane genome Saccharum spontaneum L as an example. The genome is 8-ploid with 32 chromosomes (2n = 4x8 = 32)

Download the tutorial for CDS and GFF annotation files

mkdir -p wgd_tutorial && cd wgd_tutorial
wget http://www.life.illinois.edu/ming/downloads/Spontaneum_genome/Sspon.v20190103.cds.fasta.gz
wget http://www.life.illinois.edu/ming/downloads/Spontaneum_genome/Sspon.v20190103.gff3.gz
gunzip *.gz

First conda activate wgdstart our analysis environment, and then start the analysis

Step 1 : Use to wgd mclidentify homologous genes in the genome

wgd mcl -n 20 --cds --mcl -s Sspon.v20190103.cds.fasta -o Sspon_cds.out

Step 2 : Use to wgd ksdbuild Ks distribution

wgd ksd --n_threads 80 Sspon_cds.out/Sspon.v20190103.cds.fasta.blast.tsv.mcl Sspon.v20190103.cds.fasta

Step 3 : If the quality of the genome is good, then wgd syncollinearity analysis can be used . It can help us find the collinearity block in the genome and the corresponding anchor point

wgd syn --feature gene --gene_attribute ID \
-ks wgd_ksd/Sspon.v20190103.cds.fasta.ks.tsv \
Sspon.v20190103.gff3 Sspon_cds.out/Sspon.v20190103.cds.fasta.blast.tsv.mcl

For more reading - There are 9 sub-modules in WGD

kde: KDE fitting to the Ks distribution
ksd: Ks distribution construction
mcl: BLASP comparison of All-vs-ALl + MCL classification analysis.
mix: Hybrid modeling of Ks distribution.
pre: preprocess the CDS file
syn: Call I-ADHoRe 3.0 to use GFF files for collinearity analysis
viz: draw histogram and density plot
wf1: Ks standard analysis procedure of the whole genome paranome (paranome), call mcl, ksd and syn
wf2: Ks standard analysis procedure of one-vs-one homologous gene (ortholog), call wcl and kSD

Josefa González Lab

Thu, 19 Aug 2021 08:52:56 -0500

Lab focus on understanding how organisms adapt to their environments. They combine omics approaches with detailed molecular and phenotypic analyses to get a comprehensive picture of adaptation. Our aim at being internationally recognized as a leading lab in the field of environmental adaptation.
Lab share our passion for science with the general public by leading outreach projects aimed at increasing science awareness.

More at https://www.biologiaevolutiva.org/gonzalez_lab/

Refseq viraal genome sequences !

Jit — Sat, 11 Dec 2021 08:35:18 -0600

List of all viruses on NCBI

https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/

Address of the bookmark: https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/

CrossMap: program for genome coordinates conversion between different assemblies

Rahul Nayak — Tue, 25 Jan 2022 17:59:32 -0600

CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF.

Address of the bookmark: http://crossmap.sourceforge.net/

Monkeypox virus isolate MPXV_USA_2022_MA001, complete genome

Jit — Tue, 26 Jul 2022 06:21:07 -0500

LOCUS       ON563414              197205 bp    DNA     linear   VRL 30-MAY-2022
DEFINITION  Monkeypox virus isolate MPXV_USA_2022_MA001, complete genome.
ACCESSION   ON563414
VERSION     ON563414.3
KEYWORDS    .
SOURCE      Monkeypox virus (monkeypox)
  ORGANISM  Monkeypox virus
            Viruses; Varidnaviria; Bamfordvirae; Nucleocytoviricota;
            Pokkesviricetes; Chitovirales; Poxviridae; Chordopoxvirinae;
            Orthopoxvirus.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/nuccore/ON563414

bacLIFE: an automated genome mining tool for identification of lifestyle associated genes

BioStar — Fri, 15 Mar 2024 04:59:14 -0500

bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and biosynthetic gene clusters associated with each lifestyle detected. This whole process is divided into different modules:

Clustering module Predicts, clusters and annotates the genes of every input genome
Lifestyle prediction Employs a machine learning model to forecast bacterial lifestyle or other specified metadata
Analitical module (Shiny app) Results from the previous modules are embedded in a user-friendly interface for comprehensive and interactive comparative genomics.

You can find the complete wiki here [https://github.com/Carrion-lab/bacLIFE/wiki/bacLIFE-wiki]

Address of the bookmark: https://github.com/Carrion-lab/bacLIFE

Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?

Rahul Agarwal — Wed, 17 Jul 2013 15:25:09 -0500

Like in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?