Solution-Align sequences shown below using smith-waterman

Align sequences shown below using smith-waterman algorithm

Reference no: EM131952089

1) Provide detailed reasoning for the following statement. For comparison/alignment of closely related species BLOSUM80 is a better choice than BLOSUM62.

2) Align two sequences shown below using Smith-Waterman algorithm.
Use match score of 4, mismatch score of -4 and gap penalty score of 2.
Show:

a) dynamic programming matrix with scores (as it shown in Figure 2.6 in Durbin et al.)

b) trace back pointers

c) total score
sequences:
sequence 1:
AGAGCTCACAA
sequence 2:
AGTAGCTTCCAAA

Verified Expert

This assignment is related to finding out closely related species in bioinformatics. There are different methods to do it but what the assignment wants is using the block substitution matrix method. Here we need to construct the dynamic programming matrix and find out the matching and mismatch in the sequences. Then using the matrix we can find out the similarity in any two given sequences. The matrix can be traced back and pointers can be created. Finally a similarity score can be assigned.

Reference no: EM131952089

Questions Cloud

Analyze how the use of technology has impacted communication : analyze how the use of technology has impacted organizational communication both positively and negatively.

Describe the skills needed to thoughtfully engage the client : Describe the skills needed to thoughtfully engage your client/consumer through a change experience, keeping in mind cultural awareness.

What are some best practices we can do personally : What are some best practices we can do personally to improve our personal security and help us to minimize risk of identity theft or other criminal activity?

Covered call option and a naked call option : Explain the difference between a covered call option and a naked call option. Which option entails greater risk to the investor?

Align sequences shown below using smith-waterman algorithm : Provide detailed reasoning for the statement. For comparison/alignment of closely related species BLOSUM80 is a better choice than BLOSUM62

Calculate the option exercise value : The exercise price on a put option is $40 and the price of the underlying stock is also $40. The option will expire in 55 days.

Explain the corporate governance : Explain corporate governance and its relation to integrated audits. The response must be typed, single spaced.

Plot of the net power pattern in the x-y plane : ELEC 3320 MATLAB Project. Plot of the net power pattern in the x-y plane. Design parameters will be based on the last four digits of your student ID

Determining the cash conversion cycle : The company's payables deferral period (accounts payable divided by daily purchases) is 30 days. What is C&K's cash conversion cycle?

User Account

All Pages

Align sequences shown below using smith-waterman algorithm

Reference no: EM131952089

Reference no: EM131952089

Questions Cloud

Reviews

Write a Review

Science Questions & Answers

Journal of pharmaceutical sciences

Optical fibres

Micro organisms

Describing histology of an organ

Interpret the sensitivity of mammography

Discuss the role that science plays in your daily life

Prepare a flexible budget gator divers

Neurological disorders

Complexity of cell surfaces

Exploratory activity on bird beaks

Spatial and temporal variation of heat content in the upper

Earthquake databases

Assured A++ Grade

Academics

Major Subjects

Majors

Get In Touch

TERMS & POLICIES

HELP & SUPPORT