The document describes algorithms for sequence alignment, including the Needleman-Wunsch algorithm for global alignment and the Smith-Waterman algorithm for local alignment. It provides examples of filling in a scoring matrix according to the algorithms' recurrence relations and tracing back to find the optimal alignment between two sequences.
Merge sort is a sorting technique based on divide and conquer technique. With worst-case time complexity being Ο(n log n), it is one of the most respected algorithms.
Merge sort first divides the array into equal halves and then combines them in a sorted manner.
A presentation on prim's and kruskal's algorithmGaurav Kolekar
This slides are for a presentation on Prim's and Kruskal's algorithm. Where I have tried to explain how both the algorithms work, their similarities and their differences.
Merge sort is a sorting technique based on divide and conquer technique. With worst-case time complexity being Ο(n log n), it is one of the most respected algorithms.
Merge sort first divides the array into equal halves and then combines them in a sorted manner.
A presentation on prim's and kruskal's algorithmGaurav Kolekar
This slides are for a presentation on Prim's and Kruskal's algorithm. Where I have tried to explain how both the algorithms work, their similarities and their differences.
[Question Paper] Electronic and Communication Technology (Revised Course) [Ap...Mumbai B.Sc.IT Study
This is a Question Papers of Mumbai University for B.Sc.IT Student of Semester - I [Electronic and Communication Technology] (Revised Course). [Year - April / 2014] . . .Solution Set of this Paper is Coming soon..
[Question Paper] Electronic and Communication Technology (Revised Course) [Ap...Mumbai B.Sc.IT Study
This is a Question Papers of Mumbai University for B.Sc.IT Student of Semester - I [Electronic and Communication Technology] (Revised Course). [Year - April / 2014] . . .Solution Set of this Paper is Coming soon..
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
Introduction to Memory Effects: The sources of Memory Effects in Power Amplifiers. What the root cause is and a mathematical representation of amplifier transfer function.
More: Circuit Interactions, Dynamic Non-Linear Characterization and conclusions.
See more at linamptech.com
2. Where we left off
• Output from Sequencing:
AACTGACCTA…
CCGTTGGCAT…
TTTGCGGTCA…
…
…
3. Where we left off
• I have hundreds of millions of short
• Most applications need to figure out where they
came from
• Given a reference genome sequence and millions of
short sequences, how do I figure out where each of
the short sequences came from?
4. What is an algorithm?
• A process or set of rules to be followed in
calculations or other problem-solving operations,
esp. by a computer
• X = 2 * n
• Make a burrito
• Unwrap burrito
• Place on plate in microwave
• Turn microwave on for 2 minutes
5. What makes a good algorithmic
solution?
• Speed
• Memory
• Optimality of answer
6. The alignment problem
• Input
• Two sequences s and t of length n and m
• Output
• An alignment between the two sequences with gaps
inserted appropriately
• Objective Function
• A scoring function that weights particular character to
character alignments
7. How fast do I have to eat?
• Input
• # of sandwiches
• Output
• Sandwiches / minute
• Objective function
• Minimize the number of sandwiches I have to eat per
minute such that I finish all sandwiches in an hour
8. Scoring Function
• Which alignment of ACCTG and ACTTG is better?
• AATAC AATA-C
• ATATC -ATATC
• How did you decide?
• Example scoring function:
• +1 for matches
• -1 for gaps and mismatches
11. Rules
• Fill in top row and left-most column according to
scoring function
• Start in the upper left-most corner of unfilled squares
• Move left to right filling in the result of the scoring
function
• Break ties arbitrarily
• Trace back from bottom right corner to upper left
corner
45. Rules
• Fill in top row and left-most column according to
scoring function
• Start in the upper left-most corner of unfilled squares
• Move left to right filling in the result of the scoring
function
• Break ties arbitrarily
• Trace back from the max element in the matrix to the
first STOP
46. Rules
• Fill in top row and left-most column according to
scoring function
• Start in the upper left-most corner of unfilled squares
• Move left to right filling in the result of the scoring
function
• Break ties arbitrarily
• Trace back from the max element in the matrix to the
first STOP
79. How to evaluate statistical
significance?
• Everyone pick a number between 1 and 10 (keep it
to yourself!)
80. The problem with databases
• Query is: ACCT
• Is a match significant?
• Database A:
• ACCT
• CAGG
• AAAA
• Database B:
• ACCT
• ACCT
• ACCT
81. Alignment Projects
• Research BWA
• Research Bowtie
• Research MAQ
• Code a program in the language of your choice that
performs Needleman-Wunsch or Smith Waterman