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Under program selection, the user can choose to optimize blastn for the type of sequence search that best relates to their problem, for highly similar sequences (megablast), more dissimilar sequences (discontiguous megablast)or somewhat similar sequences (blastn). At the bottom of the web page, there is a link that allows the user to view the default values for formatting (return the descriptions for the top 100 scoring alignments) and for the algorithm parameters. If you selected megablast, optimize for highly similar sequences, the word size used in the search will automatically default to 28 nucleotides. If you select blastn to optimize for somewhat similar sequences the word size will be 11 nucleotides, the historically common default value for blastn.For the purposes of this example, select to optimize for somewhat similar sequences (blastn) and click on the BLAST button to submit your query to the BLAST queue.BLAST should state that the query was successfully submitted, and provide a request ID that accesses the results. The page updates itselfautomatically, you do not have to refresh it.

The results begin with a graphical overview that uses the query sequence as therule, shown separately at the top of the graph. In this example, the rule (our query sequence) is 453 nucleotides in length. The score of each alignmentis divided into one of 5 ranges by the five different colors in the color key provided, and the alignments are placed in the order of best scores first. Thescores are normalized, and normalized scores are given in units of bits, to allow comparisons between alignments. More information on scores can andshould be perused in the Altschul tutorial on the NCBI website. Clicking on any of thefirst 50 lines in the graph takes the user to the associated alignment, located in the last section of this resultspage.

Look at the graph of best results at the top of the page. How long is the alignment length for the best match in the graph?

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The second section of the results page, immediately following the graph, contains the top 100 alignment scores and their sequence descriptions. Here, the "hits", or matched sequences returned as a list of results, contain links to their GenBank entries, their GenBank definitions under the column entitled "Accession", the normalized scores ofthe alignments, and the E-values. The E-values quantify the probability that the listed alignment might occur randomly. The scores are linked to the actual alignment further down the page. Clicking on a score will take you directly to the alignment that obtained that score.In some cases, there are icons containing capital letters in the links column, which are links to related entries in one of the NCBI databases, such as UniGene unique gene cluster information , Entrez Gene and GEO gene expression and hybridization array data . Look at the first 5 "hits" in the results list.

What organism is the most common source of the sequences in the first 5 hits?

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What protein is most commonly identified in the description column of the alignments as being associated with or related to these sequences?

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Questions & Answers

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
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'?
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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
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
hi
Loga
what does nano mean?
Anassong Reply
nano basically means 10^(-9). nanometer is a unit to measure length.
Bharti
Difference between extinct and extici spicies
Amanpreet Reply
how did you get the value of 2000N.What calculations are needed to arrive at it
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in a comparison of the stages of meiosis to the stage of mitosis, which stages are unique to meiosis and which stages have the same event in botg meiosis and mitosis
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Researchers demonstrated that the hippocampus functions in memory processing by creating lesions in the hippocampi of rats, which resulted in ________.
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The formulation of new memories is sometimes called ________, and the process of bringing up old memories is called ________.
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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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