Pairwise Alignment (Part 1)

Check 2 types of sequence alignment

• Global alignment

• Local alignment

• Universal alignment

• Specific alignment

Global alignment is based on ________________

• Needleman-Wunsch algorithm

• Smith-Waterman algorithm

• Dot Matrix algorithm

• Dynamic algorithm

It only finds local regions with the highest level of similarity between the two sequences and aligns these regions without regard for the alignment of the rest of the sequence regions.

This is the description for ____________

• Local alignment

• Global alignment

• Specific alignment

• Universal alignment

Comparing two genes with same function (in human vs. mouse).

This is the application example of ___________

• Global alignment

• Local alignment

• Universal alignment

• Specific alignment

There are three (3) primary methods in pairwise sequence alignment. They are:

• Dot matrix method

• Dynamic programming algorithm

• K-tuple method

• Iterative method

• Operative method

The statements below are about dot matrix analysis method EXCEPT:

• It is the most conventional analysis in pairwise alignment.

• The dots appear as colorless dots in the computer screen.

• Dot matrix method is a quantitative.

• Simple analysis to analyze the sequences.

DNA Sequencing

• Determining the order of nucleotides
• DNA Synthesis
• Chromosome mapping
• All of the above

This database is produced at the National Centre for Biotechnology and Information (NCBI) as the part of the International Nucleotide sequence Database collaboration (or) INSDC.

• Genbank

• Uniprot

• phylip

• perl

This method is useful in large-scale database searches to find whether there is significant match available with the query sequence.

• Dot matrix analysis

• Dynamic programming algorithm

• Word method

• Iterative method

Find the CORRECT statement about dynamic programming.

• Choice of scoring rule can dramatically influence the sequence alignments obtained

• Uses scoring matrix to quantify scores for matches, mismatch, and gap

• It is used in the database search tools FASTA and the BLAST family

• This method is a qualitative and simple to analyze sequences.

• Smith-Waterman truncates all negative scores to 0.