webPRC: the Profile Comparer for alignment-based searching of public domain databases

Abstract

Profile–profile methods are well suited to detect remote evolutionary relationships between protein families. Profile Comparer (PRC) is an existing stand-alone program for scoring and aligning hidden Markov models (HMMs), which are based on multiple sequence alignments. Since PRC compares profile HMMs instead of sequences, it can be used to find distant homologues. For this purpose, PRC is used by, for example, the CATH and Pfam-domain databases. As PRC is a profile comparer, it only reports profile HMM alignments and does not produce multiple sequence alignments. We have developed webPRC server, which makes it straightforward to search for distant homologues or similar alignments in a number of domain databases. In addition, it provides the results both as multiple sequence alignments and aligned HMMs. Furthermore, the user can view the domain annotation, evaluate the PRC hits with the Jalview multiple alignment editor and generate logos from the aligned HMMs or the aligned multiple alignments. Thus, this server assists in detecting distant homologues with PRC as well as in evaluating and using the results. The webPRC interface is available at http://www.ibi.vu.nl/programs/prcwww/.

Experimental and bioinformatic evidence that raspberry leaf blotch emaravirus P4 is a movement protein of the 30K superfamily

“…However, more powerful similarity detection methods have been developed recently, which rely on profile-profile comparisons, such as HHpred (Hildebrand et al, 2009), HHblits (Remmert et al, 2012) HHalign (Biegert et al, 2006), FFAS (Jaroszewski et al, 2011) and WebPRC (Brandt & Heringa, 2009). In brief, a sequence profile is a representation of a multiple sequence alignment that contains information about which amino acids are 'tolerated' at each position of the alignment, and with which probability.…”

Effects of error-correction of heterozygous next-generation sequencing data

“…FFAS [6] was based on a new procedure for profile generation that takes into account all the relations within the family. Some online servers are available, including FORTE [7], RANKPOOP [8], webPRC [9], PHYRE [10], GenThreader [11], COMA [12], and, Bioshell [13]. …”

Recovering full-length viral genomes from metagenomes

“…If the sequence similarity of a part of the viral target genomes to sequences in the databases is low, it is sometimes still possible to apply remote homology detection methods (Kuchibhatla et al, 2014 ), such as PSI-BLAST and HMMER3 (Altschul, 1997 ; Finn et al, 2011 ) and profile-profile comparison (HHpred Kuchibhatla et al, 2014 ), HHblits (Remmert et al, 2012 ), FFAS (Jaroszewski et al, 2011 ), WebPRC (Brandt and Heringa, 2009 ). To apply remote homology detection it is necessary that the viral family of the target genome was identified, for example by the identification of a highly conserved stretch, and that sequence profiles of this families are present in the respective databases [e.g., in pFAM (Finn et al, 2014 ) or Uniprot (Magrane and Consortium, 2011 )] or can be produced from multiple sequence alignments.…”