Recuperació de la informació Bioinformatics. Sequence and genome analysis David W. Mount Flexible Pattern Matching in Strings (2002) Gonzalo Navarro and.

Slides:



Advertisements
Presentaciones similares
-go Verbs There is a small but very important group of verbs that we call the -go verbs. These verbs are: Conocer : to know (people) Hacer: to make/do.
Advertisements

More Stem-Changing Verbs! There are two more groups of stem- changing verbs that we want to learn: the e > i and the o > ue.
-go Verbs There is a small but very important group of verbs that we call the -go verbs. These verbs are: Hacer: to make/do Poner: to put Decir: to say.
-go Verbs There is a small but very important group of verbs that we call the -go verbs. These verbs are: Hacer: to make/do Poner: to put Salir: to leave.
Hoy es jueves el seis de noviembre
Los verbos estar y ser “to be”
Verb Conjugations Easier than you think.
Spanish Interrogatives. Who? ¿Quién? Who? (multiple people) ¿Quiénes?
E-I Pedir ayuda = To ask for help -Yo pido ayuda en la clase -Tu pides ayuda en la casa -Juancho pide ayuda todos los dias -Nosotros pedimos ayuda -Ellos.
-go Verbs There is a small but very important group of verbs that we call the “-go” verbs. These verbs are: Hacer: to make/do Poner: to put Salir: to.
VOCABULARIO #2.4 ¡Aprenda! Forming Questions Señora Sequin.
Question words question WORDS? Cómo Cuándo Cuánto Dónde Por qué Qué Cuál Quién A qué hora Adónde.
Future. Before learning to form the future it in English: I will speak. The future tense in English ALWAYS has the word “will” (or “shall”). It can be.
-go Verbs There is a small but very important group of verbs that we call the “-go” verbs. These verbs are: Hacer: to make/do Poner: to put Salir: to.
Telling Time.
Peace in Marriage. Hope Keeping Christ at the center.
Objective: I can recognize and accurately use gender agreement. Do Now: Match the following Spanish and English words: 1. Pelirroja a. Good-looking 2.
POR QUÉ VS. PORQUE. ¿Por qué? = Why? *Note the accent on the letter e. * Also note that it is two separate words.
Time Expression with Hacer Grammar Essential #106.
Notes #18 Numbers 31 and higher Standard 1.2
To compare people or things that are equal to one another, you use: Making comparisons En mi club, levantar pesas es tan popular como correr.
Spanish Interrogatives. Who? ¿Quién? Who? (multiple people) ¿Quiénes?
Superlatives Grammar Essential #54. What are superlatives? Superlatives are made when one object/one group is compared to a larger group of many objects.
What has to be done today? It can be done in any order. Make a new ALC form Do the ALC Get two popsicle sticks Get 16 feet of yarn. That is 4 arms width.
Direct Object Pronouns. Direct object pronouns are simply words that replace a direct object. In English, there are two – “it” and “them”. Look at these.
Unidad 3 Leccion 1 Vocabulario.
Superlatives Español 2-2 Sra. Carpinella. What are superlatives? Superlatives are made when one object/one group is compared to a larger group of many.
Definite & indefinite articles
¿Qué haces en la escuela? Question words, objects, yo-go’s.
Talking about weather Discussing the weather is a very human thing to do, and every language has its own way of doing it. If you think about it, the weather.
Vámonos Write how many of each object appears in each picture Example: dos lápices Hoy es el dieciocho de septiembre.
-go Verbs There is a small but very important group of verbs that we call the “-go” verbs. These verbs are: Hacer: to make/do ( not on worksheet so add.
-go Verbs There is a small but very important group of verbs that we call the “-go” verbs. These verbs are: Conocer : to know (people) Hacer: to make/do.
-go Verbs There is a small but very important group of verbs that we call the “-go” verbs. These verbs are: Decir: to say/tell Hacer: to make/do Poner:
Time Telling time is rather easy. You only need to know the numbers up to 59 to be able to tell the time.
EL VERBO GUSTAR 9/9/2013 SPANISH 1 SRA. BALDWIN. GUSTAR Gustar is a Spanish verb that means “to be pleasing to”. In English, it’s kind of like saying.
Español I 4B 1. Is it a regular verb, a stem changing verb, or an irregular verb? It’s a stem changing verb!
Spanish Sentence Structure How can we make better sentences?
El calentamiento - el 6 de octubre 1.el bolígrafo la bolígrafo 2.la carpetaslas carpetas 3.el deporteslos deportes 4.el plumala pluma 5.las animaleslos.
Essential ?: How do I conjugate this irregular verb and how is it used?
Capítulo 3.  The verb ir is an irregular verb.  It follows the same pattern as an –ar verb conjugation except in the yo form even though it is an –ir.
-go Verbs There is a small but very important group of verbs that we call the “-go” verbs. These verbs are: Conocer : to know (people) Hacer: to make/do.
MY WAY Frank Sinatra MARILYNMONROEMARILYNMONROE Ligue o som.
La pregunta: ¿Cómo se dice… Please Thank you Good Evening …en Español? La tarea:  Study  Test  jueves; el 12 de septiembre (Thursday; September 12 th.
Essential ?: How do I use these irregular verbs? How are they different than the verbs I already know?
El presente indicativo ESPAÑOL 1. A. What is the present tense? It is when the action of a verb occurs at the moment. Verbs can be divided into two categories:
¿Qué le duele?. ¿Cómo formamos las frases? The verb “doler” (to hurt) is a stem changing verb. The o changes to ue in all form but the nosotros and vosotros.
El Verbo “GUSTAR” En español gustar means “to be pleasing” In English, the equivalent is “to like”
-go Verbs There is a small but very important group of verbs that we call the “-go” verbs. These verbs are: Hacer: to make/do Poner: to put Traer: to.
To be, or not to be? Let’s start out with one of the most important verbs in Spanish: ser, which means “to be.”
Telling Time in Spanish
Hazlo Ahora Answer the questions about the following paragraph: Me llamo Ixchel. Hace tres años, soy un jugador del equipo de voleibol. Yo soy un buen.
-go Verbs There is a small but very important group of verbs that we call the “-go” verbs. These verbs are: Hacer: Poner: Salir: Tener : Traer: Venir:
Forming Questions ¡Aprenda! Forming Questions By Patricia Carl October 2013.
¡Bienvenidos a clase! lunes, el 6 de abril. ¿Que vamos a hacer hoy? 1.tener + que + infinitive 2.hace + time expressions 3.adverbios.
¡Bienvenidos a clase! viernes, el 30 de octubre.
LunesMartesMiércolesJuevesViernes 1. Nadar Escuchar música2. Ir al ensayo Escuchar música3. Nadar Escuchar música4. Ver videos Escuchar música5. Salir.
Conjugate –cer/-cir/-ger/-gir/ -guir verbs in the present tense.
Verbs like Gustar Notes/ Examples.
Essential question: How do I conjugate these new verbs and use them?
Time Expression with Hacer Grammar Essential #106.
100 Book Challenge Desafío de leer 100 libros. Cada niño tendrán: Una bolsa de libros Una carpeta 2 libros para leer cada noche Un informe de lectura.
Time Expressions with Hacer
Present Tense of -ar Verbs. Regular Verb Regular Verb: follows a pattern for conjugation. Pattern: Stem + endings.
Present Tense of -er & -ir Verbs. Regular Verb Regular Verb: follows a pattern for conjugation. Pattern: Stem + endings.
To be, or not to be? Let’s start out with one of the most important verbs in Spanish: ser, which means “to be.”
To be, or not to be? Let’s start out with one of the most important verbs in Spanish: ser, which means “to be.”
Kindergarten Spanish High Frequency Words
How to use “Gustar”.
Transcripción de la presentación:

Recuperació de la informació Bioinformatics. Sequence and genome analysis David W. Mount Flexible Pattern Matching in Strings (2002) Gonzalo Navarro and Mathieu Raffinot Algorithms on strings (2001) M. Crochemore, C. Hancart and T. Lecroq

String Matching String matching: definition of the problem (text,pattern) depends on what we have: text or patterns Exact matching: Approximate matching: 1 pattern ---> The algorithm depends on |p| and |  | k patterns ---> The algorithm depends on k, |p| and |  | The text ----> Data structure for the text (suffix tree,...) The patterns ---> Data structures for the patterns Dynamic programming Sequence alignment (pairwise and multiple) Extensions Regular Expressions Probabilistic search: Sequence assembly: hash algorithm Hidden Markov Models

String matching: one pattern There is a sliding window along the text against which the pattern is compared: How does the matching algorithms made the search? Pattern : Text : Which are the facts that differentiate the algorithms? 1.How the comparison is made. 2.The length of the shift. At each step the comparison is made and the window is shifted to the right.

Alg. Cerca exacta d’un patró (text on-line) Algorismes més eficients (Navarro & Raffinot) |  | Long. patró Horspool BNDM BOM BNDM : Backward Nondeterministic Dawg Matching BOM : Backward Oracle Matching w

Autòmata Factor Oracle Factor Oracle of word G T A T G T A : GGATT AT T A G All states are final ==> Recognize all the factors … and more GGATT AT T A G Hip: recognize all the factors of GTA This new state recognizes all the factors that ends in the fourth character that cannot be recognized before. Recognize all the factors of the prefix of length four recognize all the factors.

Autòmata Factor Oracle: algorisme Algorithm: for i=1 to p do Afegir transicions que reconeguin factors acabats a i; ?

Autòmata Factor Oracle: algorisme Que passa si el següent caràcter existeix? T T

Autòmata Factor Oracle: algorisme Que passa si el següent caràcter no existeix? T T

Autòmata Factor Oracle: exemple d’algorisme GGATT AT T A G and it recognizes words that are not factors like GTGTA. But, if the automaton doesn’t recognize  it’s not a factor! That’s the strategy of the BOM algorithm.

Algorisme BOM (Backward Oracle Matching) Com es determina la següent posició de la finestra? Com fa la comparació? Text : Patró : Autòmata: Factor Oracle Comproba si el sufix és factor del patró a Si la a no s’ha trobat Si arriben a l’estat final de l’autòmat amb la a a

Autòmata Factor Oracle: exemple d’algorisme Es construeix l’autòmata del patró invers: Suposem que el patró és ATGTATG I la cerca sobre el text :G T A C T A G A A T G T G T A G A C A T G T A T G G T G A... A T G T A T G Com fa la comparació? GGATT AT T A G

Autòmata Factor Oracle: exemple d’algorisme Es construeix l’autòmata del patró invers: Suposem que el patró és ATGTATG I la cerca sobre el text :G T A C T A G A A T G T G T A G A C A T G T A T G G T G A T G T A T G Com fa la comparació? GGATT AT T A G A T G T A T G

Autòmata Factor Oracle: exemple d’algorisme Es construeix l’autòmata del patró invers: Suposem que el patró és ATGTATG I la cerca sobre el text :G T A C T A G A A T G T G T A G A C A T G T A T G G T G A T G T A T G Com fa la comparació? GGATT AT T A G A T G T A T G

Autòmata Factor Oracle: exemple d’algorisme Es construeix l’autòmata del patró invers: Suposem que el patró és ATGTATG I la cerca sobre el text :G T A C T A G A A T G T G T A G A C A T G T A T G G T G A T G T A T G Com fa la comparació? GGATT AT T A G A T G T A T G

Autòmata Factor Oracle: exemple d’algorisme Es construeix l’autòmata del patró invers: Suposem que el patró és ATGTATG I la cerca sobre el text :G T A C T A G A A T G T G T A G A C A T G T A T G G T G... A T G T A T G Com fa la comparació? GGATT AT T A G A T G T A T G

Autòmata Factor Oracle: exemple d’algorisme Es construeix l’autòmata del patró invers: Suposem que el patró és ATGTATG I la cerca sobre el text :G T A C T A G A A T G T G T A G A C A T G T A T G G T G... A T G T A T G Com fa la comparació? GGATT AT T A G A T G T A T G

Feedback: Política de privacidad Feedback
Do Not Sell My Personal Information
Sobre el proyecto: SlidePlayer Condiciones de uso

© 2024 SlidePlayer.es Inc. All rights reserved.