Reference no: EM132798681

1. Which aspect(s) of sequence alignment make this a valuable bioinformatics endeavor?

Facilitates meaningful visualization for BLAST query results

Allows inference of function based on similarity to sequences with known function

Provides an algorithmic framework to automatically process multiple sequences

Provides the best way to predict protein function

2. If two (similar length) protein sequences align so that most positions are identical:

These proteins likely have similar functions; Differing amino acids are "less conserved" than identical ones.

These proteins may function differently but the common amino acids will have the same functions.

These proteins likely have similar functions, based on the differing amino acids.

These proteins likely have different functions, based on the identical amino acids.

3. What are some applications where sequence alignment (of some kind) is important?

Mapping next generation sequencing reads to a reference genome, i.e. "re-sequencing"

Determining assay specificity, for example design of PCR primers

Predicting the secondary structure of RNA (e.g. single strand nucleic acids)

All of the above

4. What is the difference between Global Aligment and Local Alignment? What are the famous (named) algorithms associated with identifying the optimal cases of each?

5. When would one use a global alignment and/or a local alignment?

Both alignments are valuable and can provide useful information for any pair-wise alignment of sequences, regardless of sequence sizes. 

Global: Any pair of sequences, so long as there are computational resources.

Local: Sequences where you expect short identical stretches

Global: Similar-size sequences, such a proteins.

Local: Different size sequences, where query likely includes part(s) similar to (larger) target.

Global: Different size sequences, where query likely includes part(s) similar to (larger) target.

Local: Similar-size sequences, such a proteins.

6. In a simple base-identity dot-plot, what represents an optimal alignment? (score is 1 if bases i and j are the same, and 0 otherwise) 

The set of dots that are colored and contiguous, where color denotes score.

The graph path along the diagonal with the highest number of '1' elements

The graph path with the smallest number of off-diagonal elements scoring '1'

It is not possible to generalize this; You need an alignment algorithm.

7. What does the BLOSUM62 alignment score matrix represent mathematically?

Acceptability of amino acid substitutions based on aligned "blocks" in proteins with 62% identity or less.

An amino acid model for protein evolution that also serves as a scoring matrix for sequence alignments.

Scoring model for comparison of protein or nucleotide sequences, for example with BLAST.

Commonality of amino acid residues based on aligned peptides with 62% identity.

8. The BLAST parameter "word size" has what effects on search speed and sensitivity? (Word size sets "seed" match length; Sensitivity is the fraction of truly similar sequences returned for a search with a given query)

Speed increases with word size.

Sensitivity decreases with word size.

Speed decreases with word size.

Sensitivity increases with word size.

Speed and sensitivity increases with word size.

Speed and sensitivity decrease with word size.

9. What is the difference between genetics and genomoics

Genetics is the study of trait inheritance while genomics considers the whole of an organism's DNA

Genetics is the study of genes related to disease, while genomics considers the whole of an organism's DNA

Genomics is the study of single "genes" while genetics considers the whole of an organism's DNA, especially association of genotypes with phenotypes.

Genetics and genomics basically study the same domains, except one is traditional and focused and one is newer, enabled by technology, and global.

10. In terms of genome location, what does sequencing accomplish? 

Locates duplicate regions and genetic loci mutations within a chromosome structure.

Locates genome features such as gene inheritance patterns and variants.

Locate the position of heritable traits within the context of a chromosomal genetic map.

Locate the position of gene (i.e. trait-associated) sequences within the context of a genome

11. Compared to "traditional" Sanger sequencing, features associated with "Next-Gen" sequencing technologies (e.g. Illumina) include? 

Similar per-experiment cost and throughput, but easier and faster sample prep and better accuracy

Lower cost, similar throughput, somewhat shorter reads, greater accuracy.

Lower cost, higher throughput, easier sample prep, but generally shorter reads.

Lower cost, higher throughput, longer reads, reduced errors and easier genome assembly

12. Define and relate "Read", "Contig", "Scaffold" and "Assembly" with regard to deciphering a genome sequence

In the context of gene-finding, what does ORF stand for.

Operon Reading Frequency

Open Resequencing Frame

Operational Reading Frame.

Open Reading Frame.

13. How many potential "reading frames" are there for a given genomic sequence?

2

3

6

Depends on the organism

14. Which of the following represent genome annotation tracks (e.g. for a broswer)?

Repeat elements

Gene structure and exons

GC content and "CpG islands"

All of the above