Address of the bookmark: http://msaprobs.sourceforge.net/homepage.htm#latest

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign

Address of the bookmark: https://github.com/molbio-dresden/flexidot

This also includes:

• A2Amapper: ATAC, Assembly to Assembly Comparision tool:
  • Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).

• Sim4db:
  • Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.

• LEAFF:
  • LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.

• Meryl:
  • An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer

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

The ongoing 2014 West Africa Ebola outbreak is considered to be the largest and longest outbreak ever recorded of Ebola, killing at least 932 people and infecting more than 1,700 till date since March in Sierra Leone, Guinea, Nigeria and Liberia.

Hence, the World Health Organisation (WHO) on 8 August, 2014 declared the killer Ebola epidemic ravaging parts of West Africa an international health emergency.

Causes

EVD is caused by infection with a virus of the family Filoviridae, genus Ebolavirus. While there are five identified sub-species of Ebolavirus, four viruses cause disease in humans. They are Bundibugyo virus (BDBV), Ebola virus (EBOV), Sudan virus (SUDV), Taï Forest virus (TAFV).

The fifth virus, Reston virus (RESTV), is not considered to be disease-causing in humans.

According to WHO, EVD first appeared in 1976 in two simultaneous outbreaks, in Nzara, Sudan, and in Yambuku, Democratic Republic of Congo. The latter was in a village situated near the Ebola River from which the disease takes its name.

How does it spread?

It is still unclear how Ebola spreads. However, it is believed that the first pateint becomes infected through contact with an infected animal's body fluids.

Human-to-human transmission can occur through direct contact with blood, organs or other body fluids of infected people or exposure to objects such as needles and syringes that have been contaminated with infected secretions.

Ebola can also be transmitted from men who have recovered from the disease through semen as it is infectious for up to 7 weeks.

Infected dead bodies can spread Ebola as they are still infectious. So mourners who have direct contact with the body of deceased person can also get the disease.

Who is most at risk?

Health-care workers who do not wear appropriate protective clothing and family members who are in close contact with infected people or deceased patients.

Signs and symptoms:

Symptoms may occur between 2 and 21 days after contracting the infection. Common signs of Ebola include:

Fever

Headache

Muscle, abdominal and joint pain

Sore throat

Weakness

Diarrhea

Vomit or cough up blood

Chest pain

Difficulty in breathing and swallowing

Rash

Hiccups

Bleeding inside and outside the body

Prevention

Currently there is no vaccine available for humans. But the infection can be controlled through the use of recommended protective measures such as:

Avoid contacting infected blood or secretions, including from those who are dead .

Using standard precautions for all patients in the healthcare setting.

Sterilizing equipment, and wearing protective clothing including masks, gloves, gowns and goggles.

Washing your hands with soaps or detergents.

Disinfecting your surroundings.

Isolate people who have Ebola symptoms.

Culling of infected animals, with close supervision of burial or incineration of carcasses.

Yet, not travelling to the areas or countries where the virus is found is the best way to avoid Ebola.

https://www.cdc.gov/poxvirus/monkeypox/response/2022/world-map.html

Address of the bookmark: https://www.cdc.gov/poxvirus/monkeypox/response/2022/world-map.html

That is the problem ViralQC (https://github.com/ChengPENG-wolf/ViralQC) aims to solve.

Viral sequences recovered from metagenomic data can be incomplete or contaminated with microbial DNA. ViralQC uses information from both DNA sequences and predicted proteins to detect contamination and estimate how complete a viral contig is.

The authors compared ViralQC with CheckV and found that ViralQC performed particularly well for longer viral contigs, improving contamination detection and completeness estimation in several test cases.

Why does this matter? Because discovering a viral sequence is only the first step. If the sequence is contaminated or incomplete, downstream analyses—such as identifying viral functions or studying evolution—can be misleading.

ViralQC provides a useful quality check before researchers trust the viral genome they have discovered.

In a world where metagenomics is uncovering enormous numbers of unknown viruses, tools like ViralQC help us separate the real viral story from an incomplete or mixed-up one.

More at https://academic.oup.com/bioinformatics/article/42/Supplement_2/btag463/8767288

Annotation

https://bigd.big.ac.cn/ncov/variation/annotation

Genome wharehouse 

https://bigd.big.ac.cn/gwh/browse/index

Released Genome

https://bigd.big.ac.cn/ncov/release_genome

Download data 

ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/

Raw data

https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae

Address of the bookmark: https://bigd.big.ac.cn/ncov/about