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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

Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
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
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
what school?
biomolecules are e building blocks of every organics and inorganic materials.
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
sciencedirect big data base
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.
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
how to know photocatalytic properties of tio2 nanoparticles...what to do now
Akash Reply
it is a goid question and i want to know the answer as well
characteristics of micro business
for teaching engĺish at school how nano technology help us
Do somebody tell me a best nano engineering book for beginners?
s. Reply
there is no specific books for beginners but there is book called principle of nanotechnology
what is fullerene does it is used to make bukky balls
Devang Reply
are you nano engineer ?
fullerene is a bucky ball aka Carbon 60 molecule. It was name by the architect Fuller. He design the geodesic dome. it resembles a soccer ball.
what is the actual application of fullerenes nowadays?
That is a great question Damian. best way to answer that question is to Google it. there are hundreds of applications for buck minister fullerenes, from medical to aerospace. you can also find plenty of research papers that will give you great detail on the potential applications of fullerenes.
what is the Synthesis, properties,and applications of carbon nano chemistry
Abhijith Reply
Mostly, they use nano carbon for electronics and for materials to be strengthened.
is Bucky paper clear?
carbon nanotubes has various application in fuel cells membrane, current research on cancer drug,and in electronics MEMS and NEMS etc
so some one know about replacing silicon atom with phosphorous in semiconductors device?
s. Reply
Yeah, it is a pain to say the least. You basically have to heat the substarte up to around 1000 degrees celcius then pass phosphene gas over top of it, which is explosive and toxic by the way, under very low pressure.
Do you know which machine is used to that process?
how to fabricate graphene ink ?
for screen printed electrodes ?
What is lattice structure?
s. Reply
of graphene you mean?
or in general
in general
Graphene has a hexagonal structure
On having this app for quite a bit time, Haven't realised there's a chat room in it.
what is biological synthesis of nanoparticles
Sanket Reply
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
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Mueller 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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