Question

An all-against-all analysis requires first making a database of the proteome. This database is then sequentially searched by each individual protein sequence of the proteome using a rapid database similarity search tool such as _______

(a) XPBLAST

(b) WU-BLAST

(c) BLAST

(d) FASTA

This question was posed to me during an interview.

My doubt stems from Sequence Assembly and Gene Identification in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics

Answer 1

Right choice is (a) XPBLAST

The explanation: P values of WU-BLAST are similar to E values of NCBI BLAST (Rubin et al. 2000) for values of P and E < 0.05. This analysis generates a matrix of alignment scores, each with an E value and corresponding alignment for each pair of proteins. Also, the E value of an alignment score is the probability that an alignment score as good as the one found would be observed between two random or unrelated sequences in a search of a database of the same size.