What is alignment: Definition and 83 Discussions

In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
Sequence alignments are also used for non-biological sequences, such as calculating the distance cost between strings in a natural language or in financial data.

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  1. Y

    Alignment of micro dipoles in magnetic material in external magnetic field.

    I just want to verify that the dipole moment \vec{m} in the presence of external magnetic field \vec{B} will line up in the the same direction and parallel with the external field. This is according to the right hand rule that if magnetic field is the direction of the thumb, the current will...
  2. K

    Quasar Alignment to Cosmic Strings

    A very interesting but speculative paper was published in the Physical Review and arXiv recently about the possibility of the former existence of Cosmic Strings at the point of Electroweak energies. Robert Poltis and Dejan Stojkovic http://prl.aps.org/abstract/PRL/v105/i16/e161301...
  3. L

    What is the Galactic Alignment?

    I know it only happens every 26,000 years, and the sun lines up with the center of the milky way, but is this real or not? And i know it has something to do with the 2012 phenomenon?
  4. J

    Axis Alignment in Einstein's 1905 Paper: Symmetry Impact

    In Einstein's 1905 paper he says that, by reasons of symmetry, we can assume the coordinate axis of the stationary and moving frame are aligned. If the y and z axis rotate towards/away from the x-axis in the moving frame in a way dependent upon the velocity, how does this break the symmetry...
  5. E

    Pythagoras theorem - Shaft alignment TIR

    Homework Statement I am going the do some alignment of a shaft.I use a dial indicator for measurement, and use rim-face techniques. Then I need do calculate the total TIR (Total Indicated Runout). Here is my result of my measurement (Dial indicator). Top: 0 Right: +0,08 Bottom: -0,27...
  6. C

    Speed up a image alignment function using FFT

    Homework Statement I need to speed up a image alignment function using FFT Homework Equations FFT, correlation coefficient (for deciding best alignment) The Attempt at a Solution This function works but a fail to see how it is any better that a naive evaluation of the correlation...
  7. E

    LaTeX Solve Your Latex Alignment Problem | Tips for Right-Aligned Equations

    Hello, How to write the equations in Latex right-aligned? regards
  8. D

    Planetary Alignment (nothing to do with astrology)

    *THIS IS AN ACTUAL QUESTION, NOT A WHAT IF SCENARIO* I just wondered if it has ever happened or could ever happen that all of the planets align? I'm not saying there are any consequences thereof, just want to know if it's realistically possible, why/why not. Basically just because I think it...
  9. R

    Galactic Alignment: Explaining 2012 Hype

    I keep hearing people talking about this as if they know what they are talking about. Would someone enlighten me? Something tells me this could not happen, but I cannot explain what I'm thinking as I am not an astrophysicist or anything. I'm referring to the 2012 hype.
  10. S

    Polarization calculation, frame alignment

    Polarization calculation, "frame alignment" problem statement A ray of light (represented by a Stokes vector; coming from a light source) goes through an ideal polarizing filter and reflects off two surfaces (X2 and X1, in that order) and . The goal is to calculate what the stokes vector looks...
  11. R

    Planetary Alignment: Will It Affect Us?

    Ok. Let me start off by saying I don't believe 2012 is the end of everything. :smile: However, I have heard about this "planetary alignment" that is suppose to take place. Apparently, scientists have said that either they don't know what affect this will have on us, or that everyone is just...
  12. wolram

    Mirror Alignment: Keck Telescope Instrument Accuracy

    I saw part of a documentary about the keck telescope, they used an instrument that vibrated if any thing came near it to align the mirror segments, this instrument has fantastic accuracy apparently, can anyone tell me what it is called please.
  13. X

    Molecular spin alignment having macro torque effects?

    Hello, If a magnetic field aligns the electron or nuclear spins can that have a macro effect of causing torque? So for example if we had a rod and we fixed one end but allowed it to freely rotate and then aligned electron or nuclear spins would that cause the rod to rotate? Thanks, Xerxes73
  14. T

    Medical Alignment checks of the light and X-ray fields

    I was doing a first year imaging lab (in radiography course). We were supposed to check the alignment of the collimation light, and how accurate it represents the x-ray "beam". One of the question in the task question is to determine "the x-ray fields (express this answer in cm and a percentage...
  15. C

    Solving Orbital Plane Alignment of Two Planets

    Im trying to solve (approximately) the following problem: Suppose that i have 2 planets with mass m1 and m2 orbiting around the sun and i take into account the following interactions: a) Interaction between planet 1 and the sun b) Interaction between planet 2 and the sun c) Interaction...
  16. T

    Align Stack: What, Why & How for x86 Processors

    What is alignment of a stack? And why is it important to align a stack when working on an x86 processor?
  17. W

    DNA Sequence Alignment: Understanding Smith-Waterman Algorithm

    Hi all, I'm interested in learning more about DNA sequence alignment and have been reading up on the topic online. I'm more interested in the Smith-Waterman algorithm for local alignment, but I'm quite confused about how the algorithm works. I know the algorithm works on a MxN matrix...
  18. Loren Booda

    When was the last time all inner planets aligned in our solar system?

    Within the uncertainty of solar system models and their computation, what and when was the closest occurrence (in terms of solid angle) of the inner eight planets forming a radial alignment outward from the Sun?
  19. N

    LaTeX Solving Latex Alignment Problem

    Hi guys, I want to write up some math and have the following code: \begin{align} L_{A}(s)&=V(A,0)-V(A,s) \\ &=\int_{t=A}^{T(A)+A-\alpha S_{A}}e^{-r(t-A)}W_{t}dt - \int_{t=A}^{T(A)+A-\alpha (S_{A}+s)}e^{-r(t-A)}W_{t}dt \\ &=\int^{T(A)+A-\alpha...
  20. MathematicalPhysicist

    How Can I Use %nd in printf to Align Table Columns in C?

    my assignment is as follows: write a programme printing a reasonably sized table of powers, in a nice format. using %nd in printf will write an integer in at least n charcaters. this facilitates printing tables with aligned columns. here's my code: #include <stdio.h> #define STOP 10 int...
  21. S

    Magnetic alignment in a strong B-field

    Homework Statement The question is on the behavior of the magnetic and spin axes in a strong B-field (the Paschen-Back Effect, I believe it's called. Anyway...). I've got almost everything nailed down, except for one thing. In the example I've looked up...
  22. G

    Atom and Electron Cloud Alignment

    I was wondering if there is a way to align an atoms electron cloud-orbit/probability of location to one side of an electron. For example the probability of the electron being on the closet side or being in a regular area at a regular time. i.e. regular orbit area, and or keeping the electrons on...
  23. O

    Finding the Exact Time of Alignment of Earth, Sun and Center Sun

    Ok so if the center sun of our gallaxy is in sagattarius then what degree is it in sagattarius. If the Earth and the sun and the center sun were in aline once a year then would I have to see the oppisite consalation of sagattarius at the oppisite degree of the center sun in the center of the...
  24. Q

    Optics: polarisation alignment

    With a combination of wave plates in the order \lambda/2 - \lambda/4 - \lambda/2 it should be possible to achieve any polarisation. But I don't understand why: the first wave plate switches the polarisation direction, the second changes linear to circular polarisation and vice versa, and the...
  25. P

    Printer Alignment: HP PSC 2410 Photosmart

    I recently switched cartridges but forgot to re-align the printer. As a result each time I print, the words are a bit blurry. My printer is 'hp psc 2410 photosmart'. How can I re-align?
  26. M

    How does the magnetic field alignment process work?

    Hi everyone, I have a question about the mechanics of the magnetic field alignment process. If you suddenly subject some iron filings to a magnetic field, they align along the magnetic field lines. I'd like to know how this happens step by step. I understand that the iron filings which were...
  27. CarlB

    Alignment of Quasar Polarizations 0507274

    Mapping extreme-scale alignments of quasar polarization vectors Accepted by Astronomy & Astrophysics; 19 pages, 17 figures. Include Table A1 which will be available via CDS D. Hutsemekers, R. Cabanac, H. Lamy, D. Sluse Based on a new sample of 355 quasars with significant optical...
  28. P

    Planetary Alignment on my Date of Birth

    Would someone direct me to a specialist, website or any other way of find out how the planets were aligned on my date of birth. I was born August 03, 1978 at 10:07am. I want a tattoo of all the 9 planets (including the sun and the Earth moon) as they were aligned on my date of birth. Can...
  29. Arctic Fox

    Total Eclipse of the Sun: 40s Before Alignment

    Why do total eclipses of the Sun by the Moon reach maximum eclipse about 40 seconds before the Sun and Moon's gravitational forces align? :bugeye:
  30. W

    Aligning 2 Sequences using Needleman-Wunsch

    I tryed to align two sequences CCATTGGAGTA and CATAGA using Needleman-Wunsch algorithm but it only gives me 2 alignment resutls CCATTGGAGTA C-A-T--AG-A and CCATTGGAGTA C-AT---AG-A while I thought it should be 4 results because the first C in the second sequence is also permutable...
  31. S

    MATLAB MATLAB Help - Aligning Two Matrices

    Hi all I'm new to MATLAB and am having trouble with a certain function, called score. I've looked at this for a while now and can't see where I am going wrong?! The function scores the similarities of two matrices, 1 for a match -1 for a non match the code: function s =...
  32. K

    Solving the Challenge of Multiple Alignment with 4000 Sequences

    How do i do a Multiple Alignment with 4000 sequences. offline version of ClustalW hangs online version accepts only 500 sequences What is the maximum number of sequences that can be given to CluatalW ? Any other gud softw . PLease let me know ...
  33. M

    What Does Each Element in a BLAST Protein Alignment Mean?

    I am trying to do this protein alignment assignment for my Biotech class and I'm having trouble interpreting the results. I used the Blast program at [PLAIN]www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html[/URL] and have to answer the following questions: What are "Query" and "Sbjct"?, What do the...
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