This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Localized Alignments in Sequences”.
1. Which of the following is not among the methods for finding localized sequence similarity?
a) Profile Analysis
b) Block Analysis
c) Extraction of Blocks from a Global or Local MSA
d) Pattern blocking
Explanation: Pattern Searching is the correct name of the method for finding localized sequence similarity. This type of analysis was performed on groups of related proteins, and the amino acid patterns that were located may be found in the Prosite catalog.
2. Profiles are found by performing the _____ MSA of a group of sequences and then removing the _______ regions in the alignment into a smaller MSA.
a) local, more highly conserved
b) global, low conserved
c) global, more highly conserved
d) local, low conserved
Explanation: Profiles are found by performing the global MSA of a group of sequences and then removing the more highly conserved regions in the alignment into a smaller MSA. A scoring matrix for the MSA, called a profile, is then made. The profile is composed of columns much like a mini-MSA and may include matches, mismatches, insertions, and deletions.
3. The program Profilemake can be used to produce a profile from a MSA
Explanation: A version of the Profilesearch program, which performs a database search for matches to a profile, is available at the University of Pittsburgh Supercomputer Center. A special grant application may be needed to use this facility. Profile-generating programs are available by FTP and are included in the Genetics Computer Group suite of programs.
4. Which of the following is untrue regarding the block analysis method?
a) Blocks represent a conserved region in the MSA
b) Blocks differ from profiles in lacking insert and delete positions in the sequences
c) Every column includes only matches and mismatches
d) Blocks may be made by searching for a section of an MSA alignment that is low conserved
Explanation: Like profiles, blocks may be made by searching for a section of an MSA alignment that is highly conserved. However, aligned regions may also be found by searching each sequence in turn for similar patterns of the same length. These patterns may include a region with one or a few matching characters followed by a short spacer region of unmatched characters and then by another set of a few matching characters, and so on, until the sequences start to be different.
5. Block analysis methods use substitution matrices such as the PAM and BLOSUM matrices to score matches.
Explanation: these methods do not use substitution matrices such as the PAM and BLOSUM matrices to score matches. Rather, they are based on finding exact matches that have the same spacing in at least some of the input sequences, and that may be repeated in a given sequence.
6. In the method of extraction of blocks from a global or local MSA, a global MSA of related protein sequences usually includes regions that have been aligned without gaps in any of the sequences.
Explanation: These ungapped patterns may be extracted from these aligned regions and used to produce blocks. Blocks found in this manner are only as good as the MSA from which they are derived. A global MSA of related protein sequences usually includes regions that have been aligned without gaps in any of the sequences.
7. Which of the following is not true regarding the BLOCKS?
a) Blocks of width 10–55 are extracted from a protein MSA
b) The protein MSA is up to 400 sequences
c) The program doesn’t accept manually reformatted MSAs
d) The program accepts FASTA format
Explanation: The program accepts FASTA, CLUSTAL, or MSF formats, or manually reformatted MSAs. Several types of analyses may be performed with such extracted blocks. The BLOCKS server primarily generates blocks from unaligned sequences. The eMOTIFs server similarly extracts motifs from MSAs in several MSA formats and provides a formatter for additional MSA formats.
8. The pattern searching method type of analysis was performed on groups of related proteins, and the amino acid patterns that were located may be found in the Prosite catalog.
Explanation: This Prosite catalog groups proteins that have similar biochemical functions on the basis of amino acid patterns such as those in the active site. Subsequently, these families were searched for amino acid patterns by the MOTIF program (Smith et al. 1990), which finds patterns of the type aa1 d1 aa2 d2 aa3, where aa1 and aa2 are conserved amino acids and d1 and d2 are stretches of intervening sequence up to 24 amino acids long.
9. Although MOTIF program is used successfully for making the BLOCKS database, it is limited in the pattern sizes that can be found.
Explanation: The MOTIF program distinguishes true motifs from random background patterns by requiring that motifs occur in a number of the input sequences and tend not to be internally repeated in any one sequence. As the length of the motif increases, there are many possible combinations of patterns of a given length where only a few characters match.
10. Which of the following is not true regarding the BLOCKS?
a) The BLOCKS server can extract a conserved, ungapped region from a MSA to produce a sequence block
b) The server can also find blocks in a set of unaligned, input sequences and maintains a large database of blocks based on an analysis of proteins in the Prosite catalog
c) Blocks are found by the Protomat program
d) The program MOTIF doesn’t locate spaced patterns
Explanation: Blocks are found in two steps: First, the program MOTIF described on the previous page is used to locate spaced patterns. The second step takes the best and most consistent patterns found in step 1 and uses the program MOTOMAT to merge overlapping triplets and extend them, orders the resulting blocks, and chooses those that are in the largest subset of sequences.
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