Protein threading, also known as fold recognition, is a method of protein modeling (i.e. computational protein structure prediction) which is used to model those proteins which have the same fold as proteins of known structures, but do not have homologous proteins with known structure. It differs from the homology modeling method of structure prediction as it (protein threading)
is used for proteins which do not have their homologous protein structures deposited in the Protein Data Bank (PDB), whereas homology modeling is used for those proteins which do. Threading works by using statistical knowledge of the relationship between the structures deposited in the PDB and the sequence of the protein which one wishes to model. Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the “target” protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the “template”). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence.

Correct Option: C

Protein threading, also known as fold recognition, is a method of protein modeling (i.e. computational protein structure prediction) which is used to model those proteins which have the same fold as proteins of known structures, but do not have homologous proteins with known structure. It differs from the homology modeling method of structure prediction as it (protein threading)
is used for proteins which do not have their homologous protein structures deposited in the Protein Data Bank (PDB), whereas homology modeling is used for those proteins which do. Threading works by using statistical knowledge of the relationship between the structures deposited in the PDB and the sequence of the protein which one wishes to model. Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the “target” protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the “template”). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence.

• BOXSHADE is a program for pretty-printing multiple alignment output. The program itself doesn't do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE. Of course, you can also use manually aligned sequences (in a proper format).
• BCM Launcher, i.e. Baylor College of Medicine Search Launcher is an on-going project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters). It helps in finding alignments.
• PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins.
• BOXSHADE is a program for pretty-printing multiple alignment output. The program itself doesn't do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE. Of course, you can also use manually aligned sequences (in a proper format).
• BCM Launcher, i.e. Baylor College of Medicine Search Launcher is an on-going project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters). It helps in finding alignments.
• PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins.

Correct Option: D

• BOXSHADE is a program for pretty-printing multiple alignment output. The program itself doesn't do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE. Of course, you can also use manually aligned sequences (in a proper format).
• BCM Launcher, i.e. Baylor College of Medicine Search Launcher is an on-going project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters). It helps in finding alignments.
• PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins.

Orthologs, or orthologous genes, are genes in different species that originated by vertical descent from a single gene of the last common ancestor. Paralogous sequences provide useful insight into the way genomes evolve. The genes encoding myoglobin and hemoglobin are considered to be ancient paralogs.

Correct Option: C

Orthologs, or orthologous genes, are genes in different species that originated by vertical descent from a single gene of the last common ancestor. Paralogous sequences provide useful insight into the way genomes evolve. The genes encoding myoglobin and hemoglobin are considered to be ancient paralogs.

In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold.

Correct Option: B

In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold.

• UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a simple agglomerative or hierarchical clustering method. Inbioinformatics, UPGMA is used for the creation of phenetic trees (phenograms). In a phylogenetic context, UPGMA assumes a constant rate of evolution (molecular clock hypothesis).
• CLUSTAL is a general purpose multiple sequence alignment program for DNA or proteins.
• SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation(such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc), a minimal level of redundancy and a high level of integration with other databases.
• RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures

Correct Option: B

• UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a simple agglomerative or hierarchical clustering method. Inbioinformatics, UPGMA is used for the creation of phenetic trees (phenograms). In a phylogenetic context, UPGMA assumes a constant rate of evolution (molecular clock hypothesis).
• CLUSTAL is a general purpose multiple sequence alignment program for DNA or proteins.
• SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation(such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc), a minimal level of redundancy and a high level of integration with other databases.
• RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures