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Before looking at the alignment in Jalview, look at the text results.

Which 2 sequences align with the highest pairwise alignment score?

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Look at the text display of the alignments, shown just below the scores. Try to determine the regions where the 6 sequences align most closely.Many people find this type of text display hard to interpret (a fact that is good to remember when putting together a figure for a presentation or anarticle). At the bottom of the text display is a cladogram. A cladogram is a branched phylogenetic-type tree where the branches are of equal length.Cladograms can show common ancestry, but because the branches have equal lengths, they do not provide an accurate indication of the evolutionarydistance between the branches.

Does the cladogram group together all the human CFTR sequences in the same branch?

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Now, look at the alignment in Jal view. Is it easier to identify the regions where all6 sequences align most closely in the Jalview display?

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Leave both of these windows open (closing the ClustalW text results browser page may cause the Jalview editor pageto disappear automatically). Notice the file number assigned this Jalview sequence alignment. This is to help distinguish it for purposes of comparison from the nextand last alignment in this tutorial, where the gap penalty will be manipulated from the default values.

Finally, repeat the CFTR alignment using the sequences above, but this time change "Gap Open" to 100.(Click on the term "Gap Open" to view the default value.) This will increase the penalty for opening a gap. For more information on gaps and gap penalties,view the EBI help page entitled "About Gaps" . Compare the group alignment scores from the previous alignment with these groupalignment scores. The group alignment scores can be found in the .output file (listed in the results section) under the section which starts:

Start of Multiple Alignment There are 5 groupsAligning...

Does changing the gap open penalty affect the group alignment scores?

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Are the group scores higher or lower when the penalty is increased to 100?

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View the Jalview display of the new alignment. Compare the Jalview displays of the first alignment,and the new alignment with the increased gap penalty, in the regions numbered 1220 to 1250.

Describe the differences in the two alignments in this region, both in terms of the gaps, and in terms of the similarity bargraph displayed below the sequences.

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A look at the ClustalW submission page is enough to see that there are many more parameters that can be manipulated by the user. However, the default values have been optimized and generally should be left alone, except in cases where the user has a definitive justification for making the change. It does frequently occur in biology, though, that the user knows some empirical information that conflicts with the results given by an alignment performed with the default values. In these cases, a scientific argument can be made for altering the parameters to force the alignment to reflect the empirical information.

Questions & Answers

where we get a research paper on Nano chemistry....?
Maira Reply
what are the products of Nano chemistry?
Maira Reply
There are lots of products of nano chemistry... Like nano coatings.....carbon fiber.. And lots of others..
learn
Even nanotechnology is pretty much all about chemistry... Its the chemistry on quantum or atomic level
learn
Google
da
no nanotechnology is also a part of physics and maths it requires angle formulas and some pressure regarding concepts
Bhagvanji
Preparation and Applications of Nanomaterial for Drug Delivery
Hafiz Reply
revolt
da
Application of nanotechnology in medicine
what is variations in raman spectra for nanomaterials
Jyoti Reply
I only see partial conversation and what's the question here!
Crow Reply
what about nanotechnology for water purification
RAW Reply
please someone correct me if I'm wrong but I think one can use nanoparticles, specially silver nanoparticles for water treatment.
Damian
yes that's correct
Professor
I think
Professor
Nasa has use it in the 60's, copper as water purification in the moon travel.
Alexandre
nanocopper obvius
Alexandre
what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
Rafiq
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
Damian
How we are making nano material?
LITNING Reply
what is a peer
LITNING Reply
What is meant by 'nano scale'?
LITNING Reply
What is STMs full form?
LITNING
scanning tunneling microscope
Sahil
how nano science is used for hydrophobicity
Santosh
Do u think that Graphene and Fullrene fiber can be used to make Air Plane body structure the lightest and strongest. Rafiq
Rafiq
what is differents between GO and RGO?
Mahi
what is simplest way to understand the applications of nano robots used to detect the cancer affected cell of human body.? How this robot is carried to required site of body cell.? what will be the carrier material and how can be detected that correct delivery of drug is done Rafiq
Rafiq
if virus is killing to make ARTIFICIAL DNA OF GRAPHENE FOR KILLED THE VIRUS .THIS IS OUR ASSUMPTION
Anam
analytical skills graphene is prepared to kill any type viruses .
Anam
Any one who tell me about Preparation and application of Nanomaterial for drug Delivery
Hafiz
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
Bob
The nanotechnology is as new science, to scale nanometric
brayan
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Damian
Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
Renato
What fields keep nano created devices from performing or assimulating ? Magnetic fields ? Are do they assimilate ?
Stoney Reply
why we need to study biomolecules, molecular biology in nanotechnology?
Adin Reply
?
Kyle
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
Adin
why?
Adin
what school?
Kyle
biomolecules are e building blocks of every organics and inorganic materials.
Joe
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Source:  OpenStax, Bios 533 bioinformatics. OpenStax CNX. Sep 24, 2008 Download for free at http://cnx.org/content/col10152/1.16
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