Question

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

(a) Each motif or domain is represented by an HMM profile generated from the seed alignment of a number of conserved homologous proteins

(b) Since the probability scoring mechanism is more complex in HMM than in a profile-based approach the use of HMM yields further increases in sensitivity of the database matches

(c) Pfam-B only contains sequence families not covered in Pfam

(d) The functional annotation of motifs in Pfam-A is often related to that in UNIPROT

The question was asked by my college professor while I was bunking the class.

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

Answer 1

Correct option is (d) The functional annotation of motifs in Pfam-A is often related to that in UNIPROT

Explanation: Pfam is a database with protein domain alignments derived from sequences in SWISSPROT and TrEMBL. The Pfam database is composed of two parts, Pfam-A and Pfam-B. Pfam-A involves manual alignments and Pfam-B, automatic alignment in a way similar to ProDom. The functional annotation of motifs in Pfam-A is often related to that in PROSITE. Because of the automatic nature, Pfam-B has a much larger coverage but is also more error prone because some HMMs are generated from unrelated sequences.