Bioinformatics water
What is EMBOSS water?
water uses the Smith-Waterman algorithm (modified for speed enhancments) to calculate the local alignment of a sequence to one or more other sequences.
The gap insertion penalty, gap extension penalty and substitution matrix used to calculate the alignments are specified.
The output is a standard EMBOSS alignment file..
What is global sequence alignment?
A global alignment aligns two sequences from beginning to end, aligning each letter in each sequence only once.An alignment is produced, regardless of whether or not there is similarity between the sequences..
What is the difference between needle and water in EMBOSS?
Water is for aligning the best matching subsequences of two sequences.
It does not necessarily align whole sequences against each other; you should use needle if you wish to align closely related sequences along their whole lengths..
What is the full form of EMBOSS?
EMBOSS is an acronym for European Molecular Biology Open Software Suite.
The European part of the name hints at the wider scope.
The core EMBOSS groups are collaborating with many other groups to develop the new applications that the users need..
What is the purpose of EMBOSS water?
EMBOSS Water uses the Smith-Waterman algorithm (modified for speed enhancements) to calculate the local alignment of two sequences.
The default settings will fulfill the needs of most users.
More options (Click here, if you want to view or change the default settings.).
What is the role of water in the cell?
Water's extensive capability to dissolve a variety of molecules has earned it the designation of “universal solvent,” and it is this ability that makes water such an invaluable life-sustaining force.
On a biological level, water's role as a solvent helps cells transport and use substances like oxygen or nutrients..
- A global alignment aligns two sequences from beginning to end, aligning each letter in each sequence only once.An alignment is produced, regardless of whether or not there is similarity between the sequences.
- EMBOSS is an acronym for European Molecular Biology Open Software Suite.
The European part of the name hints at the wider scope.
The core EMBOSS groups are collaborating with many other groups to develop the new applications that the users need. - Local alignment • Is a matching two sequence from regions which have more similar with each other. • These are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context.
- water, a substance composed of the chemical elements hydrogen and oxygen and existing in gaseous, liquid, and solid states.
It is one of the most plentiful and essential of compounds.
A tasteless and odourless liquid at room temperature, it has the important ability to dissolve many other substances.
waterTo access a sequence from a database, enter the USA here:To upload a sequence from your local computer, select it here:To enter the sequence data
waterTo access a standard EMBOSS data file, enter the name here: (default is EBLOSUM62 for protein, EDNAFULL for nucleic)To upload a data file from your
How do scientists find harmful bacteria in water?
It consists in reviewing (or ‘sequencing’) the genetic information of most of the bacteria present in the water, which allows scientists to spot harmful species.
Both methods, however, require well-equipped laboratories with highly trained staff, making them challenging to use in remote areas.
Is in situ metagenomic water tracing a viable alternative?
eLife 10 :e61504.
While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including:
pathogens direct tracing of all aquatic DNA through metagenomics poses a profound alternative.
Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Is metagenomics a viable alternative to traditional microbiological Freshwater tests?
Accepted for publication after peer review and revision. eLife 10 :e61504.
While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including:
pathogens direct tracing of all aquatic DNA through metagenomics poses a profound alternative.
Viruses are a major cause of human waterborne and water-related diseases. Waterborne diseases are caused by water that is contaminated by human and animal urine and feces that contain pathogenic microorganisms.
A subject can get infected through contact with or consumption of the contaminated water.
Viruses affect all living organisms from single cellular plants, bacteria and animal to the highest forms of plants and animals including human beings.
Within a specific kingdom the localization of viruses colonizing the host can vary: Some human viruses, for example, HIV, colonizes only the immune system, while influenza viruses on the other hand can colonize either the upper respiratory tract or the lower respiratory tract depending on the type.
Different viruses can have different routes of transmission; for example, HIV is directly transferred by contaminated body fluids from an infected host into the tissue or bloodstream of a new host while influenza is airborne and transmitted through inhalation of contaminated air containing viral particles by a new host.
Research has also suggested that solid surface plays a role in the transmission of water viruses.
In a experiments that used E.coli phages, Qβ, fr, T4, and MS2 confirmed that viruses survive on a solid surface longer compared to when they are in water.
Because of this adaptation to survive longer on solid surfaces, viruses now have a prolonged opportunities to infect humans.
Enteric viruses primarily infect the intestinal tract through ingestion of food and water contaminated with viruses of fecal origin.
Some viruses can be transmitted through all three routes of transmission.
Viruses are a major cause of human waterborne and water-related diseases. Waterborne diseases are caused by water that is contaminated by human and animal urine and feces that contain pathogenic microorganisms.
A subject can get infected through contact with or consumption of the contaminated water.
Viruses affect all living organisms from single cellular plants, bacteria and animal to the highest forms of plants and animals including human beings.
Within a specific kingdom the localization of viruses colonizing the host can vary: Some human viruses, for example, HIV, colonizes only the immune system, while influenza viruses on the other hand can colonize either the upper respiratory tract or the lower respiratory tract depending on the type.
Different viruses can have different routes of transmission; for example, HIV is directly transferred by contaminated body fluids from an infected host into the tissue or bloodstream of a new host while influenza is airborne and transmitted through inhalation of contaminated air containing viral particles by a new host.
Research has also suggested that solid surface plays a role in the transmission of water viruses.
In a experiments that used E.coli phages, Qβ, fr, T4, and MS2 confirmed that viruses survive on a solid surface longer compared to when they are in water.
Because of this adaptation to survive longer on solid surfaces, viruses now have a prolonged opportunities to infect humans.
Enteric viruses primarily infect the intestinal tract through ingestion of food and water contaminated with viruses of fecal origin.
Some viruses can be transmitted through all three routes of transmission.
