Question

Which of the following is false in case of the database SMART and its algorithm?

(a) Contains HMM profiles constructed from manually refined protein domain alignments

(b) Alignments in the database are built based on tertiary structures whenever available or based on PSI-BLAST profiles

(c) Alignments are further checked but not refined by human annotators before HMM profile construction

(d) SMART stands for Simple Modular Architecture Research Tool

I have been asked this question in semester exam.

This intriguing question originated from Motif and Domain Databases Using Statistical Models in section Sequence Alignment of Bioinformatics

Answer 1

Correct choice is (c) Alignments are further checked but not refined by human annotators before HMM profile construction

To elaborate: Alignments are further checked and refined by human annotators before HMM profile construction. Protein functions are also manually curated. Thus, the database may be of better quality than Pfam with more extensive functional annotations. Compared to Pfam,

The SMART database contains an independent collection of HMMs, with emphasis on signaling, extracellular, and chromatin-associated motifs and domains. Sequence searching in this database produces a graphical output of domains with well-annotated information with respect to cellular localization, functional sites, super-family, and tertiary structure.