Pfam: multiple sequence alignments and HMM-profiles of protein domains

By Erik L. L. Sonnhammer, Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin. 1998

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Citations in the corpus

The HHpred interactive server for protein homology detection and structure prediction (2005, background): “Databases: A wide range of regularly updated structure and protein family databases can be searched: the PDB (21), SCOP (22), Pfam (23), SMART (24), COG (25) and CDD (26).”
Pfam: clans, web tools and services (2005, background): “One of the fundamental philosophies of Pfam is that new protein families are not allowed to overlap with existing Pfam entries (2).”
SMURF: genomic mapping of fungal secondary metabolite clusters (2010, unknown): “The corresponding de novo HMM model for this domain (TIGR03429) was created in this study from the seed alignment generated using the A. fumigatus dimethylallyl tryptophan synthase FtmPT2 as a seed sequence as previously described (Sonnhammer et al., 1998).”
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007, background): “Many of these classifications, together with various expert-curated databases [19] such as Swiss-Prot [20], Pfam [15,21], and TIGRFAM [22,23], or integrated efforts such as Uniprot [24] and InterPro [25], provide rich resources for protein annotation.”
Using Bayesian Networks to Analyze Expression Data (2000, unknown): “(1998), containing 76 gene expression measurements of the mRNA levels of 6177S. cerevisiaeORFs. These experiments measure six time series under diffe rent cell cycle synchronization methods. Spellman et al. (1998) identified 800 genes whose expression varied over the different cell-cycle stages.”
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches (2007, unknown): “org) [18,19].”
Hidden Markov Models and their Applications in Biological Sequence Analysis (2009, background): “Currently, we have two such libraries that have compiled a large number of profile-HMMs for various protein families: the PROSITE database [36, 37] and the Pfam database [38, 39].”
Polyhydroxyalkanoates: an overview. (2003, methodology): “Domains were detected by RPS-BLAST (Altschul et al., 1997) against the Conserved Domain Database (www.ncbi.nlm.nih.gov/ Structure/cdd/wrpsb.cgi) of PFAM HMMs (Sonhammer et al., 1998).”