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The third section of the results page contains the actual alignments, listed in the same order as the graphed results and the scores.

In the first alignment, what is the ratio of identical bases to total bases in the aligned subsequence?

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What is the listed percent identity?

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What is the E- (Expect) value?

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Look for entry with the accession code BC005255.1 at the beginning of the alignment and click on the accession link. Note that this "hit" is a cDNA, or a DNA sequence that has been copied from anmRNA molecule by the enzyme reverse transcriptase. This is indicated in the description, but whenever the source of the sequenceis unclear, click the link for the GI number and view the GenBank entry for more information. Look under the "COMMENT" section foradditional details about this sequence.

What group was responsible for the DNA sequencing for this entry?

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Return to the BLAST alignment results page. Scroll down to view the actual sequence alignments. The alignments are represented with vertical lines illustrating identicalmatches, blanks indicate no match. In these nucleotide alignments, there is no measurement for similarity between non-identical nucleotides. In protein alignments, however, chemical or structural similarity isusually identified between the amino acids.

Return to the BLAST home page , and select the blastx "translated nucleotide sequence query". Cut and paste the same nucleotide sequence used in theprevious example into the "Search" box. The default translation tool is BLASTX, which translates the query sequence into a protein sequence and searches a protein database. To search a translatednucleotide database with a protein query, the TBLASTN algorithm should be selected. To search a translated nucleotide database with a translated nucleotide sequence, the choice would be TBLASTX. TBLASTXis the most computationally intensive of these three searches, therefore common practice is to use BLASTX first to search protein sequence databases, and then if there are no hits withBLASTX, consider TBLASTX to translate nucleotide sequence database entries into protein sequences. For this example, use the translation algorithm BLASTX. Use the nr database and leave the default values for all other BLAST options, and hit BLAST.View the results page.

What protein is listed in the vast majority of the returned matches?

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Look at the first alignment, which should have 100% identitybetween the aligned subsequences. Note that a particular alignment may have more than one sequence associated with it. Therefore, you must look at the actual alignments, not the list of scores, to answer the following questions.

Why is the score lower for the BLASTX result than for the BLASTN result, even though the percent identity between aligned subsequences is 100%?

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How many different species are listed as sources where the aligned subsequence has an identical amino acid to total amino acid ratio of86/86, and 100% identity?

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Questions & Answers

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
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
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
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
research.net
kanaga
sciencedirect big data base
Ernesto
Introduction about quantum dots in nanotechnology
Praveena Reply
what does nano mean?
Anassong Reply
nano basically means 10^(-9). nanometer is a unit to measure length.
Bharti
do you think it's worthwhile in the long term to study the effects and possibilities of nanotechnology on viral treatment?
Damian Reply
absolutely yes
Daniel
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
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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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