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This protein sequence is highlyconserved across several species, a trait that is often a sign of physiological importance. Scroll through the protein alignments. Notice that alignmentbetween amino acids is illustrated differently than alignment between nucleotides. An identical match is shown by listing the one letter amino acidcode in the middle row, between the two aligned sequences. A mismatch is indicated by a blank, but similarity is indicated by the "+" sign, meaning theamino acids are not identical, but they have some of the same chemical or structural properties. Gaps are indicated by hyphens in the sequence that contains the gaps. Gaps are penalized in an alignment, and cause the normalized score to be lower.

BLAT , stands for Blast-like alignment tool (2), and is used forsequence comparisons against an entire genome. Review the difference between BLAT and BLAST at the BLAT FAQ site . Execute aBLAT search, using the sequence above, from the UCSC Genome Bioinformatics Site . Click on the link in this web page entitled "BLAT".Search the human genome, leaving the settings at the default values. The search results will first appear in summary form. Identify the sequence our query most closely matches by the highest score.

What human chromosome (number) contains the sequence our query most closely aligns?

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What percent identity exists between our sequence and the aligned subsequence(s)?

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Click on the link entitled "details". First, the query sequence is presented,with matching bases capitalized in blue font. Bases in cyan mark the beginning and end of aligned subsequences, indicating a gap in either the reference or the querysequence. Second, the genomic sequence from the selected chromosome is shown, and blue, capitalizedbases illustrate the matching region(s). Notice that the query cDNA sequence is missing a largeregion of DNA that is present in the chromosome. The pairwise alignment is shown below the genomic sequence. Return to the original results summary andclick on the link entitled "browser". The missing region is illustrated in graphical form here, where the chromosome band is shown in grey, extendingacross the graph and the query sequence, labeled at the left as "YourSeq", is in black, below the STS Markers.In fact, the examples in this module use an EST, or an expressed-sequence tag, for the query sequence. ESTs are mRNA-derivedrepresentations of the genes expressed in a given tissue and/or at a given developmental stage.

Knowing that our sequence is an EST, how could this explain the region of DNA that appears in the genomic sequence, but not in our query sequence?

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If the answer to this question is not intuitive, read the EST section of the NCBI primer. Scroll down to the section entitled "Genes and Gene Prediction Tracks" and change the display options under Ensembl to "pack" and the setting under GenScan to "pack". Next, scroll to the bottom of the page and hit the refresh button. (For a description of the different display options for annotation tracks, read the User Guide . The GenScan predicted genes for this area of the chromosome are shown in brown, while the Ensembl gene predictions are in maroon.

How does our sequence line up with the predicted genes?

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Now, design an independent search in order to answer the following question. What is the GI number and definition for the EST that aligns most closely with our query sequence, according to BLAST?

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This has been an introduction to BLAST sequence alignment, designed to give an idea of some of the different ways to optimize searches and problems that require the useof sequence alignment tools. Subsequent modules in this course will build on this foundation, exploring advanced techniques and additional alignment tools.

Questions & Answers

where we get a research paper on Nano chemistry....?
Maira Reply
nanopartical of organic/inorganic / physical chemistry , pdf / thesis / review
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..
Even nanotechnology is pretty much all about chemistry... Its the chemistry on quantum or atomic level
no nanotechnology is also a part of physics and maths it requires angle formulas and some pressure regarding concepts
Preparation and Applications of Nanomaterial for Drug Delivery
Hafiz Reply
Application of nanotechnology in medicine
what is variations in raman spectra for nanomaterials
Jyoti Reply
ya I also want to know the raman spectra
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.
yes that's correct
I think
Nasa has use it in the 60's, copper as water purification in the moon travel.
nanocopper obvius
what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
How we are making nano material?
what is a peer
What is meant by 'nano scale'?
What is STMs full form?
scanning tunneling microscope
how nano science is used for hydrophobicity
Do u think that Graphene and Fullrene fiber can be used to make Air Plane body structure the lightest and strongest. Rafiq
what is differents between GO and RGO?
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
analytical skills graphene is prepared to kill any type viruses .
Any one who tell me about Preparation and application of Nanomaterial for drug Delivery
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
The nanotechnology is as new science, to scale nanometric
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
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.
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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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