ArticleNucleic acids research2009
webPRC: the Profile Comparer for alignment-based searching of public domain databases.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Protein domain identification methods and online resources.Computational and structural biotechnology journal · 2021Review
- CATH: expanding the horizons of structure-based functional annotations for genome sequences.Nucleic acids research · 2019Article
- Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence.PLoS computational biology · 2016Article
- Protein remote homology detection by combining Chou's distance-pair pseudo amino acid composition and principal component analysis.Molecular genetics and genomics : MGG · 2015Article
- Recovering full-length viral genomes from metagenomes.Frontiers in microbiology · 2015Review
- Using distances between Top-n-gram and residue pairs for protein remote homology detection.BMC bioinformatics · 2014Article
- Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins.Journal of virology · 2014Article
- Using amino acid physicochemical distance transformation for fast protein remote homology detection.PloS one · 2012Article
- FFAS server: novel features and applications.Nucleic acids research · 2011Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
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/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.