--%>
Assignment Help - homework help

Sequence Alignment

What is Sequence Alignment in Homology modelling?

E

Expert

Verified

Sequence Alignment: This is the critical step in homology modeling. We have many methods for this. But we have to select a method based on our needs. We have considered some factors while choosing a method.

The factors are as bellow:

• Algorithm to be used
• Scoring matrices to be used
• Assignment of gap venalities

Homology modeling is based on dynamic programming algorithms. There are number of algorithms such as Needleman and Wunsch, Smith waterman and Blastp.The last one is different from others because it doesn’t allow any gaps. The scoring matrices of alignments are very typical matrices in which the identical amino acids are constructed in to a 20X20 matrix. We generally apply four types of general scorings to the alignments. They are:

• Identity
• Genetic code
• Chemical Similarity
• Observed Substitutions

Identity considers the residues that are identical. The genetic code considers changes in DNA and RNA which interconverts codons for the amino acids. Chemical similarity considers the physico-chemical properties with greater weight given to alignment of similar properties. The substitution frequencies observed in alignment of sequences are considered by observed substitutions. Substitution schemes are based on analysis of the frequency with which a given amino acid is observed to be replaced by another with which the sequence alignment is found, so these are considered to be the best methods of scoring alignments.

   Related Questions in Biology

  • Q : Name the subunits from which ribosomes

    Name the subunits from which ribosomes are made up of.

    		•
  • Q : Describe the deplasmolysis of plant

    Describe the deplasmolysis of plant cells?

    		•
  • Q : How Individuals Behave - Organizational

    They behave differently to different stimuli because of a multitude of factors. These include an individual's age, sex, education, intelligence, personality, physical characteristics, experience, values, and family and cultural background. For instance, a young railway ticket collector would beha

    		•
  • Q : In how many ways ELISA can be performed

    In how many ways ELISA can be performed.

    		•
  • Q : Leaders and Leadership skills Paper

    The Leaders and Leadership skills of those serving in the Armed Forces - The Struggles / Achievements Then and Now. Final paper will be 30 to 35 double spaced pages. Paper will be written in the third person and contain about 15 to 20 references or citations, which is the expectation for

    		•
  • Q : Backlash - Barriers to Diversity -

    Negative reaction to the gaining of power and influence by members of previously underrepresented groups, leading to fear, resentment, and reverse discrimination.  

    		•
  • Q : Hormones generated by the testicles and

    Name the hormones generated by the testicles and ovaries? Answer: The testicles form androgenic hormones, the major of them being testosterone. The ovaries generate

    		•
  • Q : Explain Quality Assurance or Quality

    Quality Assurance or Quality Control: The words “quality assurance” and “quality control” are frequently employed interchangeably to refer to ways of making sure the quality of a service or product. The words, however, have dis

    		•
  • Q : Abundant form in which nitrogen is

    Write down the most abundant form in which nitrogen is found in nature.

    		•
  • Q : How to make planning effective How to

    How to make planning effective While it is true that the planning suffers from several limitations, an organization cannot do without planning. The following steps s

    		•