Question

Which of the following is untrue in case of the database BLOCKS?

(a) The alignments are automatically generated using the same data sets used for deriving the BLOSUM matrices

(b) The derived ungapped alignments are called ‘blocks’, which are usually longer than motifs, are subsequently converted to PSSMs

(c) A weighting scheme and pseudo counts are subsequently applied to the PSSMs to account for underrepresented and unobserved residues in alignments

(d) The functional annotation of blocks is not consistent with that for the motifs

The question was posed to me in an interview for job.

The query is from Motif and Domain Databases Using Statistical Models in chapter Sequence Alignment of Bioinformatics

Answer 1

Right choice is (d) The functional annotation of blocks is not consistent with that for the motifs

To elaborate: BLOCKS is a database that uses multiple alignments derived from the most conserved, ungapped regions of homologous protein sequences. Because blocks often encompass motifs, the functional annotation of blocks is thus consistent with that for the motifs. A query sequence can be used to align with pre-computed profiles in the database to select the highest scored matches. Because of the use of the weighting scheme, the signal-to-noise ratio is improved relative to PRINTS.