BIOL 3220 - Intro to Bioinformatics (Ch4-#)

Iowa State University. All homework and attendance quiz questions from Ch 4 through Ch #.

E-value represents ____. It is ____ (dependent on or independent from) the subject database.

The number of random alignment that is equally good or even better than the real alignment; dependent

Enzyme A is required for lipid production in yeast. Enzyme B is the human version of enzyme A. What to be expected for the blastp results between A and B?

High percent similarity, low E-value

Frog alpha-chain gene and mouse alpha-chain gene are…

orthologs

Mouse alpha-chain gene and mouse beta-chain gene are…

paralogs

Frog alpha-chain gene and mouse beta-chain gene are…

paralogs

Which of the following information CANNOT be inferred from a phylogenetic tree?

A) The order of speciation and duplication in an evolutionary history

B) The evolutionary distance among proteins

C) The functional similarity among different proteins

D) The exact time needed for an ancestor protein evolving into a progeny protein

The exact time needed for an ancestor protein evolving into a progeny protein

The syntenic regions between human chr 1 and mouse chr 1 are labeled by the same color.

Genes A and H are homologs;

Genes D and K are homologs;

Genes E and G are homologs;

Genes F and L are homologs;

Which gene pair are syntelogs?

F and L

What is the category of mitochondria (GO:0005739)?

Cellular component

Which GO annotation has the highest confidence?

GO annotation is based on comparing the phenotypes between the wild-type and knock-out yeast strain

You performed a ChIP-seq experiment and identified 200 genes that are regulatory targets of transcription factor X.

Twenty of the target genes carry GO term A.

What is the percentage of A-genes in the input list?

10%

You performed a ChIP-seq experiment and identified 200 genes that are regulatory targets of transcription factor X.

Human genome contains ~20,000 genes, with 400 genes carrying GO term A.

What is the percentage of A-genes in the human genome?

2%

You performed a ChIP-seq experiment and identified 200 genes that are regulatory targets of transcription factor X.

Twenty of the target genes carry GO term A.

Human genome contains ~20,000 genes, with 400 genes carrying GO term A.

What is the fold enrichment of GO term A in the X-target genes?

5