Question

- _____________ is a tool for obtaining open reading frames from a cDNA sequence.

a) RPS-BLAST b) SixPack c) T-coffee d) UniGene

- Two basic ways to make a phylogenetic tree are distance-based and character-based. A fundamental difference between them is:

a) Distance-based methods essentially summarize relatedness across the length of protein or DNA sequences while character-based methods do not.

b) Distance-based methods are only used for DNA data while character-based methods are used for DNA or protein data.

c) Distance-based methods use parsimony while character-based methods do not.

d) Distance-based methods have branches that are proportional to time while character-based methods do not.

Answer 1

1.

The correct option is b - Sixpack

Sixpack is a tool from EMBOSS that reads the DNA sequences and translate the nucleic acid sequences in the frame and finds out Open Reading frames (ORF)

2.

The correct option is a - Distance-based methods essentially summarize relatedness across the length of protein or DNA sequences while character-based methods do not

The distance-based method is based on the measure of the genetic distance of the biological sequences (DNA or protein). They transform the sequence data into pairwise dissimilarities (distance) and then use the distance matrix during tree building. The character-based method is based on the characters of the sequences. They use aligned sequences such as DNA or.protein sequences directly during tree building. The character-based method includes maximum parsimony and maximum likelihood