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

    Automotive Alignment Theory - DIY Help

    It seems that "most" stock sedans do not have adjustable caster, camber and turning angle, provisions are only provided to adjust toe only. I'm trying to find a way to DIY this at home, if this is possible, and had some questions on the theory behind it. For my car, the stated toe specification...
  2. DaveC426913

    B Einstein ring has four images?

    "When the alignment is nearly perfect and the lens mass has an elliptical distribution, the background source would appear as quadruply lensed." https://www.sci.news/astronomy/esos-very-large-telescope-einstein-cross-12265.html Am i reading too much into this? Why four duplications? Is there...
  3. skaiser

    I Issues collimating my laser with 4f system

    I am using 2 lenses in a 4f configuration. The input is a large collimated beam (632nm). After passage through the 2 lenses the beams vertical dimension remains constant, however, the horizontal dimension get smaller, as if it is being focused only in the horizontal direction. Does anyone have...
  4. PainterGuy

    Text alignment in Scientific Workplace

    Hi, I'm having two serious issues with writing a document in Scientific Workplace. In Microsoft Word one can choose a paper size such as 'Letter' and Word would restrict the written sentences within the defined margins. Is it possible to do in Scientific Workplace? Is it possible to use...
  5. PainterGuy

    LaTeX Vertical space and left alignment in Latex

    Hi, How do I left align the text below? Also, how do I create vertical spaces above and below the line stating "Subbing the following expressions..."? Could you please help me with it?To derive 14(ii) m_{0} \gamma^{2} \frac{d^{2} y}{d t^{2}}=e E_{y}^{\prime} from 13(ii) m_{0} \frac{d^{2}...
  6. H

    B Uncertainty Principle versus spin alignment

    Hello, So I know that the magnetic moments of atoms are dependent on the spin and orbital angular momenta of its electrons. Both of these quantities are limited by the uncertainty principle so that neither of their direction and magnitude can be known simultaneously with arbitrary precision...
  7. qwereqe

    Detecting the Alignment of an Inf. Plane Capacitor: A Paradox?

    Assuming we have an infinite plane capacitor,where the upper plate is charged positively and the bottom layer is charged negatively. Now we know the field outside the capacitor is zero so we can't tell if the positive charge is on the upper plate or the lower plate. But, if we place it inside...
  8. aleees

    I Magnetic momentum alignment and precession

    In my lecture notes on paramagnetism and diamagnetism is stated that "according to van vleck critical considering an electron in motion around the nucleus diamagnetic and paramagnetic effect compensate (classical)" The proof following takes the intrinsic momentum related to L as the momentum...
  9. Edge5

    How does photolithography align wafers through opaque layers?

    In a lithography process I have a hard mask which is opaque. I have to make a wafer alignment, however I use optical techniques to align my wafer (lasers etc.) . How can I align my wafer through an opaque layer?
  10. B

    Earth’s magnetic field alignment and climate change?

    The Earth’s magnetic field is slowly moving with respect to the Earth’s surface and to the Sun’s incoming radiation and solar wind direction. Does the tilting/moving of Earth’s magnetic field axis to the incoming solar wind direction change the protection on different points of the Earth’s...
  11. N

    Optimizing Phase and Gain Alignment for DF Systems at 200KHz

    Hi all I have simultaneously recorded data coming from three pre-amplifiers with same input applied to these pre-amps. After post analysis, i found that there are phase and gain differences among these outputs ( which should be zero in ideal case). I set one preamplifer output as reference and...
  12. A

    Spin alignment in Magnetic Resonance Imaging

    I'm reading about the theory behind MRI, specifically from Farr's Physics for Medical Imaging, 2nd Edition, by Allisy-Roberts and Williams. According to this book, the spins of the free protons in a sample line up, either parallel or antiparallel, with the externally applied magnetic field. In...
  13. drgibbles

    Processor and Memory data alignment with base pointers?

    Hello, working on a puzzle and I think this may be what I need to do to solve it. I have a long string of characters,752 total with the range 0-9 and a-f. I believe that the data needs to be aligned based off the processor and memory. The Cpu is at 2800MHz and the memory is 1024MB. Is there a...
  14. T

    Magnetic alignment of steel question

    Hi, I have a question about steel, for instance, silicon steel used in magnetic cores. I was wondering about how Iron magnetises: can you align the grains/domains and heat treat it [or anything], so that it responds differently to flux one way then the other direction? For example, say you...
  15. wolram

    B What is the significance of the spooky alignment among quasars?

    https://www.sciencedaily.com/releases/2014/11/141119084506.htm Is this alignment spooky or is there some underlying pattern in the universe?
  16. wolram

    B Weird alignment of black holes

    In scientific daily. https://www.sciencedaily.com/releases/2016/04/160411130033.htm How can a cosmic strings align black holes , or any other process,
  17. B

    Automotive Relationship Between Tire/Wheel Size and Alignment

    As the title says, how will installing a larger tire/wheel combination or altering wheel offset change the alignment with respect to caster, camber, and toe? I know that the parameters are affected, but I cannot verbalize or visualize these changes. Feel free to use big words and jargon. TIA!
  18. Tom MS

    Does Wave Refraction Change Wave Direction or Alignment

    I can't seem to find anything online that talks about this distinction. I understand how when the water gets shallower that part of the wave gets slowed down so the overall alignment parallels with the shore. However, I wouldn't think that would change the actual direction of the wave. I need a...
  19. Andy Resnick

    Astrophotography with New Sensor - Improved Alignment & Stabilization

    Back up and running; got these last weekend. 400/2.8, 50 minutes total integration time, 10s ISO 2000 individual frames. 800/5.6, 14 minutes total, 6s ISO 2000 individual frames. It's been an adjustment to the new sensor, my alignment technique had to improve by about 2x to eliminate...
  20. P

    Alignment of the compass needle

    If a compass is placed above a current carrying wire, why does the compass needle align itself in the direction of the magnetic field produced by the wire?
  21. W

    Vertical alignment mechanism on eccentric shaft

    What would be the appropriate mechanism such that when the eccentric circle is rotating about the larger center circle the table stays horizontal? The large circular is the driver (its continuously rotating)
  22. Bandersnatch

    Nice ongoing planetary alignment

    Just bringing to everybody's attention that there's a very nice alignment of planets in the morning sky. Venus, Jupiter and Mars are within a few degrees of each other, next to the constellation of Leo. In two weeks' time, while they'll spread out a bit by then, the Moon will also swing by. If...
  23. F

    Planetary Alignment: Mercury Out of Sync

    Hi everybody, last week I was messing arround with Stelarium; I saw something which bothered me.http://postimg.org/image/l9fsnnqkv/ http://postimg.org/image/l9fsnnqkv/ (link because the image might not be seen) . As far as I know all planets rotate around the solar equator, but here, Mercury...
  24. H

    Precession of Earth's axis and alignment with stars

    I picked up a book about the pyramids at Cheops. (Relax, it wasn't a crackpot work.) It said that the pyramid was aligned with the star Polaris, and that Sirus and Orion may be sighted through some of the ventilation shafts. Now the pyramid is aligned with true north. It the time of the...
  25. T

    Matter Alignment: Magnatism Effects on Salt Water Flow

    Could a field of a certain.type of magnatism effect a giving area of salt water as to.either align or dispurse the water to more freely flow among them or slide between them .like a horizon of water molecules
  26. H

    LaTeX Latex problem with alignment character and &

    \begin{align*} AB &= \sqrt{(2-(-1))^2+(3-4)^2}\\ &= \sqrt{3^2+(-1)^2}\\ &= \sqrt{10}. \end{align*} is what i am entering. This is the error i am getting; misplaced alignment character &.I am baffled.
  27. S

    Wheel Alignment Design: Camber, Caster, & More

    Is there any formulae available for designing wheel alignment parameters like camber,caster,steering axis inclination and toe in and toe out.
  28. S

    Adjusting Accelerometer Readings for Tilt and Rotation: A Scientific Approach

    I have been using an accelerometer and I have realized that it was sitting at a tilt of 18 degrees in the z direction and rotated at 5 degrees in the x y direction. How should I change my accelerometer readings to account for this?
  29. 4

    Spin precession vs alignment in magnetic field

    The spin of an arbitrarily oriented electron precesses in the presence of a magnetic field (see Feyman lectures 10-7). The energy states also split due to magnetic fields (see Feynman lectures 12-4). I am trying to understand how to think about spin precession, spin flipping, and spin...
  30. B

    Linear alignment conveyor design

    I have a tub randomly filled with light longitudinal parts like pencils or matches. My goal is to gather them into a buffer nicely aligned (independently of which end is facing side). What's the fastest way to achieve this? I have considered unconventional bowl feeder with substantial radius...
  31. L

    Alignment of a Rotary Kiln Neck

    Hi, i´d like to ask support to solve the following problem: One of my customers has an horizontal rotary kiln, equipped with riding rings and carryings rollers. Due to some overheating of the kiln shell, nowadays the whole kiln and the kiln neck is wobbling about 70 mm (+-35 mm) around the...
  32. caters

    When Will the Planets Align Again with Varying Year Lengths?

    okay so here are the lengths of years and days on the planets: Mercury: Day: 176 Earth days Year: 88 1 year on mercury is daytime and the other is nightime Venus: Day: 243 Earth days Year: 224.7 Earth days Earth: day: 1 Earth day Year: 365 Earth days Mars: Day: 1.03 Earth...
  33. B0b-A

    Is constant planetary alignment (syzygy) possible ?

    Is a solar system possible where there was constant planetary alignment (syzygy) Let's make it the simplest scenario : just two planets orbiting a sun [the planets are different ]
  34. T

    Surface alignment of P3HT and other conductive polymers

    Hi all, It is well known that poly(3-hexyl thiophene) and other conductive polymers with alkyl substituents align when deposited on a surface (e.g. by spin coating or drop casting). The common orientations for P3HT on silicon/silicon dioxide are "edge-on" in which the alkyl side-chains point...
  35. A

    LaTeX Please help Alignment of very very long equations in latex

    Please help! Alignment of very very long equations in latex Hi all, I need to type very long equations in LATEX. \begin{equation} x = x'' + y'' + blah blah blah + z'' + blah ...\end {equation} When I compile and create the pdf , the equations(the long ones) run into the edge of the...
  36. B

    A three-gear alignment problem, simultaneous equations

    This is a problem that a few friends and I came up with while working on an extra-curricular robotics project: There are three gears meshed together with idle gears inbetween so that the three gears rotate in the same direction. http://puu.sh/2knXq The gear ratio between gear A has 4 teeth...
  37. Ackbach

    MHB (Possibly) Tricky Alignment Problem

    So, I'm typing away as follows: \begin{align*} 1.\quad &y=\sqrt{x+2}\qquad\qquad\qquad &6.\quad &x=3\\ 2.\quad &x^{2}+y^{2}=16 &7.\quad &(1,2);\;(1,4);\;(2,7)\\ 3.\quad &y=x^{2}+3x+4 &8.\quad &(1,2);\;(2,4);\;(3,6)\\ 4.\quad &y^{2}=x-3 &9.\quad &y=4\\ 5.\quad &0\le x\le 1 &10.\quad...
  38. B

    LaTeX LaTeX alignment and orientation

    LaTeX Help! Currently I writing my Thesis report using LaTeX. I have been noticing the following problem. I need the figures and text to be aligned in a page in the following orientation text figure text figure However, what I obtain is figure text text figure At times, this gets...
  39. A

    Mathematical Iteration for Alignment of 4 Points

    What is the mathematical equation or algorithm for alignment of four points in cartesian coordinates (X & Y). Say, we have 4 nominal points (Xn & Yn), and another 4 measured points (Xm & Ym)?. After alignment, what are the new locations of the measured points (Xmn & Ymn)?.
  40. P

    Time on Planet X: Solving for the Alignment of Clock Hands

    Homework Statement A wall clock on Planet X has two hands that are aligned at midnight and turn in the same direction at uniform rates, one at 4.27×10−2 rad/ s and the other at 1.62×10−2 rad/s . At how many seconds after midnight are these hands first aligned and next aligned? Homework...
  41. S

    Rotation parametrization of alignment of two vectors

    Hello, I'm looking for an appropriate rotation representation for the following situation. I have two (always non-zero) vectors, v1, v2, that may or may not be parallel. The rotation relating the two vectors is obviously non-unique having one degree of freedom, parametrized by p. So my...
  42. Fredrik

    LaTeX Multiple alignment points in LaTeX

    If I have two strings of equalities within the same align or alignat environment, and the first one is long enough to need two lines, I would want the result to look like A+B+C=D=E =F=G=H I=J rather than A+B+C=D=E =F=G=H I=J Is there a way to do this? I suppose it can be done...
  43. Vorde

    Magnetic Poles & Earth's Rotation Alignment

    Why do the magnetic poles line up (relatively speaking) with the poles of Earth's rotation?
  44. G

    Alignment of Spin in const magnetic field.

    BACKGROUND: I calculated a spin-1/2 ptl. with const magnetic field. I thought that, as time goes by, the spin should align to the direction of the magnetic field, because the energy of that state is lowest energy. but, the spin vector(expectation value) just rotates around the direction...
  45. R

    Sequence Alignment and Dynamic Programming

    Homework Statement I'm having trouble understanding dynamic programming as it relates to sequence alignments. I understand from my lecture notes that the scoring matrix used has arbitrary values (in our case +5 for match, -2 for mismatch, and -6 for gap). I therefore understand why square...
  46. R

    Neodymium ball magnet field alignment

    If a magnetised neodymium ball has a definite north and south point, could you slice the ball in two, and weld 2 "north" halves together, to create an entirely north ball? If this is impossible, how about designing a ball made in, say, a 3D printer, then embed it with small magnetised neodymium...
  47. O

    Einstein-de Haas Experiment: Magnetic Dipole Moment Alignment

    Hi. So, you surround a ferromagnet with a solenoid. Run current through solenoid to create B field withing. 2 Questions: 1:Why do the magnetic dipole moments in the ferromagnet "align" with the magnetic field of the solenoid? Doesn't lenz's law say that the magnetic field within the...
  48. Y

    Dimension alignment in a station in curve

    I have a question regarding constructing subway platforms in curved line. As we know, in a curve, wagons get out of linear alignment and become closer in inner radius and separate from each other in outer radius. I want to know the relation between dimension of car, dimension of structure...
  49. S

    Structural alignment in ferromagnetism

    Is it enough/correct to say "the atoms are aligned" in a ferromagnet, or must you specify that "the electrons (or their spin) are aligned"?
  50. Greg Bernhardt

    Is fixing car alignment important?

    My car currently veers to the right pretty heavily. I need to have the wheel turned very slightly to the left at all times for it not to run off the road. It's been that way for several months now and I'm not too bothered by it. However I just saw my shop has a deal to fix front and rear...
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