<< Chapter < Page Chapter >> Page >

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?

Got questions? Get instant answers now!

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

Got questions? Get instant answers now!

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?

Got questions? Get instant answers now!

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?

Got questions? Get instant answers now!

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?

Got questions? Get instant answers now!

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

can someone help me with some logarithmic and exponential equations.
Jeffrey Reply
sure. what is your question?
okay, so you have 6 raised to the power of 2. what is that part of your answer
I don't understand what the A with approx sign and the boxed x mean
it think it's written 20/(X-6)^2 so it's 20 divided by X-6 squared
I'm not sure why it wrote it the other way
I got X =-6
ok. so take the square root of both sides, now you have plus or minus the square root of 20= x-6
oops. ignore that.
so you not have an equal sign anywhere in the original equation?
Commplementary angles
Idrissa Reply
im all ears I need to learn
right! what he said ⤴⤴⤴
what is a good calculator for all algebra; would a Casio fx 260 work with all algebra equations? please name the cheapest, thanks.
Kevin Reply
a perfect square v²+2v+_
Dearan Reply
kkk nice
Abdirahman Reply
algebra 2 Inequalities:If equation 2 = 0 it is an open set?
Kim Reply
or infinite solutions?
The answer is neither. The function, 2 = 0 cannot exist. Hence, the function is undefined.
Embra Reply
if |A| not equal to 0 and order of A is n prove that adj (adj A = |A|
Nancy Reply
rolling four fair dice and getting an even number an all four dice
ramon Reply
Kristine 2*2*2=8
Bridget Reply
Differences Between Laspeyres and Paasche Indices
Emedobi Reply
No. 7x -4y is simplified from 4x + (3y + 3x) -7y
Mary Reply
is it 3×y ?
Joan Reply
J, combine like terms 7x-4y
Bridget Reply
im not good at math so would this help me
Rachael Reply
I'm not good at math so would you help me
what is the problem that i will help you to self with?
how do you translate this in Algebraic Expressions
linda Reply
Need to simplify the expresin. 3/7 (x+y)-1/7 (x-1)=
Crystal Reply
. After 3 months on a diet, Lisa had lost 12% of her original weight. She lost 21 pounds. What was Lisa's original weight?
Chris Reply
what's the easiest and fastest way to the synthesize AgNP?
Damian Reply
types of nano material
abeetha Reply
I start with an easy one. carbon nanotubes woven into a long filament like a string
many many of nanotubes
what is the k.e before it land
what is the function of carbon nanotubes?
what is nanomaterials​ and their applications of sensors.
Ramkumar Reply
what is nano technology
Sravani Reply
what is system testing?
preparation of nanomaterial
Victor Reply
Yes, Nanotechnology has a very fast field of applications and their is always something new to do with it...
Himanshu Reply
good afternoon madam
what is system testing
what is the application of nanotechnology?
In this morden time nanotechnology used in many field . 1-Electronics-manufacturad IC ,RAM,MRAM,solar panel etc 2-Helth and Medical-Nanomedicine,Drug Dilivery for cancer treatment etc 3- Atomobile -MEMS, Coating on car etc. and may other field for details you can check at Google
anybody can imagine what will be happen after 100 years from now in nano tech world
after 100 year this will be not nanotechnology maybe this technology name will be change . maybe aftet 100 year . we work on electron lable practically about its properties and behaviour by the different instruments
name doesn't matter , whatever it will be change... I'm taking about effect on circumstances of the microscopic world
how hard could it be to apply nanotechnology against viral infections such HIV or Ebola?
silver nanoparticles could handle the job?
not now but maybe in future only AgNP maybe any other nanomaterials
can nanotechnology change the direction of the face of the world
Prasenjit Reply
At high concentrations (>0.01 M), the relation between absorptivity coefficient and absorbance is no longer linear. This is due to the electrostatic interactions between the quantum dots in close proximity. If the concentration of the solution is high, another effect that is seen is the scattering of light from the large number of quantum dots. This assumption only works at low concentrations of the analyte. Presence of stray light.
Ali Reply
the Beer law works very well for dilute solutions but fails for very high concentrations. why?
bamidele Reply
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
Privacy Information Security Software Version 1.1a
Got questions? Join the online conversation and get instant answers!
QuizOver.com Reply

Get the best Algebra and trigonometry course in your pocket!

Source:  OpenStax, Bios 533 bioinformatics. OpenStax CNX. Sep 24, 2008 Download for free at http://cnx.org/content/col10152/1.16
Google Play and the Google Play logo are trademarks of Google Inc.

Notification Switch

Would you like to follow the 'Bios 533 bioinformatics' conversation and receive update notifications?