Class 2 Homework

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Class 2 Homework

Please answer the following questions

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Your UCSD AID (exam) number

Two sequences are said to be homologous if:

1 point

They belong to the same fold family

They have converged to share similar functional properties

Their alignments share 30% identity

They have diverged from a common ancestor

Clear selection

Orthologs are defined as:

1 point

Homologous sequences in different species that share an ancestral gene

Homologous sequences that share little amino acid identity but share great structural similarity

Homologous sequences in the same species that arose through gene duplication

Homologous sequences in the same species which have similar and often redundant functions

Clear selection

True or false: Two proteins that share 30% amino acid identity are 30% homologous.

1 point

TRUE

FALSE

Clear selection

On a new page use an ENTREZ search of the GENE database to determine the chromosomal location of the human gene for glucose-6-phosphate dehydrogenase

Use filters to focus on results for Homo sapiens - Be sure to use a new browser page!

1 point

Chromosome Y

Chromosome 7

Chromosome 11

Chromosome X

Clear selection

On a new page use an ENTREZ search to determine genes that are believed to be involved in Berardinelli-Seip syndrome.

Old discontinued records in the gene database often point to new records as information expands. Remember to use a new page for your search.

You have a DNA sequence. You want to know which protein in the main protein database (“nr,” the nonredundant database) is most similar to some protein encoded by your DNA. Which program should you use?

1 point

blastn

blastp

blastx

tblasx

Clear selection

Which of the following sentences best describes the difference between a global alignment and a local alignment between two sequences?

1 point

Global alignment is usually used for DNA sequences, while local alignment is usually used for protein sequences.

Global alignment has gaps, while local alignment does not have gaps.

Global alignment finds the global maximum, while local alignment finds the local maximum.

Global alignment aligns the whole sequence, while local alignment finds the best subsequence that aligns.

Clear selection

A global alignment algorithm (such as the Needleman– Wunsch algorithm) is guaranteed to find an optimal alignment. Such an algorithm:

1 point

Puts the two proteins being compared into a matrix and finds the optimal score by exhaustively searching every possible combination of alignments

Puts the two proteins being compared into a matrix and finds the optimal score by iterative recursions

Puts the two proteins being compared into a matrix and finds the optimal alignment by finding optimal subpaths that define the best alignment(s)

Can be used for proteins but not for DNA sequences

Clear selection

True or False: A local alignment approach is more suitable for typical database searches than a global alignment approach?

1 point

TRUE

FALSE

Clear selection

Which output from a BLAST search provides an estimate of the number of false positives?

1 point

E value

Bit score

Percent identity

Percent positives

Clear selection

Changing which of the following BLAST parameters would tend to yield fewer search results?

1 point

Turning off the low-complexity filter

Changing the expect value (E-value) from 1 to 10

Changing the expect value (E-value) from 1 to 0.05

Changing the scoring matrix from PAM30 to PAM70

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You can limit a BLAST search using any Entrez term. For example, you can limit the results to sequences from a particular organism?

0 points

TRUE

FALSE

Clear selection

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