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Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures

Andrew F Neuwald, Christopher J Lanczycki, Aron Marchler-Bauer
2012 BMC Bioinformatics  
large) multiple sequence alignment.  ...  The NCBI Conserved Domain Database (CDD) consists of a collection of multiple sequence alignments of protein domains that are at various stages of being manually curated into evolutionary hierarchies based  ...  The MAPGAPS program [48] was used to obtain accurate multiple alignments containing vast numbers of sequences starting from a curated alignment.  ... 
doi:10.1186/1471-2105-13-144 pmid:22726767 pmcid:PMC3599474 fatcat:l4utwl443bgwjbs7x7gypl2tum

Orthology prediction methods: A quality assessment using curated protein families

Kalliopi Trachana, Tomas A. Larsson, Sean Powell, Wei-Hua Chen, Tobias Doerks, Jean Muller, Peer Bork
2011 Bioessays  
We used 70 manually curated families to analyze the performance of five public methods in Metazoa.  ...  The increasing number of sequenced genomes has prompted the development of several automated orthology prediction methods.  ...  We are grateful to Lars Juhl Jensen, Martijn Huynen, Evgeny Zdobnov, and Michael Kuhn for their insightful comments, Venkata Satagopam for his help with EnsEMBL History, and all members of the Bork group  ... 
doi:10.1002/bies.201100062 pmid:21853451 pmcid:PMC3193375 fatcat:5hkwdtl77nehrjs72vlm2fxpnu

The accuracy of several multiple sequence alignment programs for proteins

Paulo A S Nuin, Zhouzhi Wang, Elisabeth R M Tillier
2006 BMC Bioinformatics  
There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences.  ...  We found that alignment accuracy is extremely dependent on the number of insertions and deletions in the sequences, and that indel size has a weaker effect.  ...  Acknowledgements We thank Daniel Lei for helping in the analysis, RL Charlebois for critical reading of the manuscript and Joy Abramson for Simprot support.  ... 
doi:10.1186/1471-2105-7-471 pmid:17062146 pmcid:PMC1633746 fatcat:2slzmchfdvccpko6jkxfkelvha

CORAL: aligning conserved core regions across domain families

Jessica H. Fong, Aron Marchler-Bauer
2009 Computer applications in the biosciences : CABIOS  
Motivation: Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families.  ...  0.45 from other methods.  ...  ACKNOWLEDGEMENTS We thank Anna Panchenko and John Spouge for helpful discussions. Funding: Intramural Research Program of the National Institutes of Health, National Library of Medicine.  ... 
doi:10.1093/bioinformatics/btp334 pmid:19470584 pmcid:PMC2712342 fatcat:ynms36o6nvcjbap2rb46axj7e4

Structure Comparison and Alignment [chapter]

Philip E. Bourne, Ilya N. Shindyalov
2005 Methods of biochemical analysis  
MAMR and EC research is supported by the European Union (Marie Curie Program FP6-039722), the Spanish Ministerio de Educación y Ciencia (BIO2007/66670), and the Generalitat Valenciana (GV/2007/065).  ...  Accurate and Fast Methods for Multiple Structure Alignment: Existing methods for multiple structure alignment are reaching unprecedented levels of coverage and accuracy.  ...  In summary, for a large number of evolutionarily related proteins, structure alignments provide valuable insights not achievable from sequence alone.  ... 
doi:10.1002/0471721204.ch16 fatcat:rehizpnzsbbjfgi7jjef6slssm

Predicting Protein Folds with Fold-Specific PSSM Libraries

Yoojin Hong, Sree Vamsee Chintapalli, Kyung Dae Ko, Gaurav Bhardwaj, Zhenhai Zhang, Damian van Rossum, Randen L. Patterson, Peter Csermely
2011 PLoS ONE  
This ability to detect distant relationships is dependent on low-identity sequence alignments obtained from FSL.  ...  Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies.  ...  Acknowledgments We would like to thank the CAC Center and Jason Holmes for their exceptional support, and to the Gozik lab for running our dataset using FFAS30.  ... 
doi:10.1371/journal.pone.0020557 pmid:21698189 pmcid:PMC3116844 fatcat:3jeaq7ecjffhjaxkbx6lsva5na

Accuracy of structure-based sequence alignment of automatic methods

Changhoon Kim, Byungkook Lee
2007 BMC Bioinformatics  
Accurate sequence alignments are essential for homology searches and for building threedimensional structural models of proteins.  ...  Results In this study, we evaluate CE, DaliLite, FAST, LOCK2, MATRAS, SHEBA and VAST in terms of the accuracy of the sequence alignments they produce, using sequence alignments from NCBI's human-curated  ...  Aron Marchler-Bauer for reading the manuscript and for the many valuable comments. We also thank the authors of CHIMERA and of the structure alignment programs for making their programs available.  ... 
doi:10.1186/1471-2105-8-355 pmid:17883866 pmcid:PMC2039753 fatcat:bt5mfakv4jdhjjtis6c263n7mi

Creation and Analysis of Protein Multiple Sequence Alignments [chapter]

Geoffrey J. Barton
2002 Methods of biochemical analysis  
Hierarchical Methods The most accurate, practical methods for automatic multiple alignment are hierarchical methods.  ...  Although many programs exist that can generate a multiple alignment from unaligned sequences, extreme care must be taken when interpreting the results.  ...  Generation of a Multiple Sequence Alignment 1. Copy the file ann rep1 frags.fa to a new directory. 2. Run CLUSTAL W on ann rep1 frags.fa.  ... 
doi:10.1002/0471223921.ch9 fatcat:brl5cvk54rgdtbuiu5douewaxa

Evaluating, Comparing, and Interpreting Protein Domain Hierarchies

Andrew F. Neuwald
2014 Journal of Computational Biology  
sequence determinants of protein function, and for genome annotation.  ...  Arranging protein domain sequences hierarchically into evolutionarily divergent subgroups is important for investigating evolutionary history, for speeding up web-based similarity searches, for identifying  ...  ACKNOWLEDGMENT This work was supported by the School of Medicine at the University of Maryland, Baltimore and by NIH contract HHSN 2630000999571.  ... 
doi:10.1089/cmb.2013.0098 pmid:24559108 pmcid:PMC3962652 fatcat:ozlal4en5zbavbohr6556kc46m

The Abundance of Short Proteins in the Mammalian Proteome

Martin C. Frith, Alistair R. Forrest, Ehsan Nourbakhsh, Ken C. Pang, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Timothy L. Bailey, Sean M. Grimmond
2006 PLoS Genetics  
Short proteins play key roles in cell signalling and other processes, but their abundance in the mammalian proteome is unknown.  ...  Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway.  ...  Acknowledgments We thank Geoffrey Faulkner for assistance with the expression profiling, Jinfeng Liu for providing the Swiss-Prot sequences in Dataset S4, and Mhairi Marshall and Sam Griffiths-Jones for  ... 
doi:10.1371/journal.pgen.0020052 pmid:16683031 pmcid:PMC1449894 fatcat:qm5xb6otgbgldfphftjyg7kfnq

Protein function annotation using protein domain family resources

Sayoni Das, Christine A. Orengo
2016 Methods  
As a result of the genome sequencing and structural genomics initiatives, we have a wealth of protein sequence and structural data.  ...  This article reviews the current approaches of protein function prediction using structure and sequence based classification of protein domain family resources with a special focus on functional families  ...  These methods invariably require an accurate multiple sequence alignment of the protein family as a starting point in their pipeline which is likely to be erroneous for very large and very diverse families  ... 
doi:10.1016/j.ymeth.2015.09.029 pmid:26434392 fatcat:mylm6k4kznalbogoxw223mfxzi

7TMRmine: a Web server for hierarchical mining of 7TMR proteins

Guoqing Lu, Zhifang Wang, Alan M Jones, Etsuko N Moriyama
2009 BMC Genomics  
Users can integrate various alignment-based, alignment-free, and TM-prediction methods in any combination and in any hierarchical order.  ...  Users can submit protein sequences for analysis, or explore pre-analyzed results for multiple genomes. The server currently includes prediction results and the summary statistics for 68 genomes.  ...  This work was in part funded by Nebraska EPSCoR Women in Science, NSF EPSCoR Type II grant, and the grant number R01LM009219 from the National Library of Medicine to E.N.M., and the NIGMS (GM65989-01),  ... 
doi:10.1186/1471-2164-10-275 pmid:19538753 pmcid:PMC2718930 fatcat:56d5ftbcwjcbvkclh3rhrynxqa

Discovering non-coding RNA elements in Drosophila 3' untranslated regions

Cuncong Zhong, Justen Andrews, Shaojie Zhang
2014 International Journal of Bioinformatics Research and Applications  
Many of the regulations are found to be triggered by RNA-protein or RNA-RNA interaction, which usually occurs in the 3′ Untranslated Regions (3′-UTRs) of the mRNA (Besse and Ephrussi,  ...  Background Post-transcriptional control is the regulation at the protein level through the existing mRNAs by modifying their stability, translation efficiency and subcellular locations.  ...  Shaojie Zhang received his PhD in Computer Science from the University of California, San Diego.  ... 
doi:10.1504/ijbra.2014.062996 pmid:24989864 pmcid:PMC4121059 fatcat:gi7zidz6qvaerp2sot36wmw73a

Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

M. R. Aniba, O. Poch, J. D. Thompson
2010 Nucleic Acids Research  
To illustrate these principles, we present a more detailed discussion of benchmarks for multiple alignments of protein sequences.  ...  As in many other domains, significant progress has been achieved in the multiple alignment field and the datasets have become progressively more challenging as the existing algorithms have evolved.  ...  ACKNOWLEDGEMENTS The authors would like to thank the members of the Laboratory of Integrative Bioinformatics and Genomics (LBGI) for many fruitful discussions and the Strasbourg Bioinformatics Platform  ... 
doi:10.1093/nar/gkq625 pmid:20639539 pmcid:PMC2995051 fatcat:nfxihponuzedjosm6cwgcccjee

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy

G P S Raghava, Stephen M J Searle, Patrick C Audley, Jonathan D Barber, Geoffrey J Barton
2003 BMC Bioinformatics  
The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is  ...  In this paper we describe a suite of reference alignments derived from the comparison of protein three-dimensional structures together with evaluation measures and software that allow automatically generated  ...  The work was subsequently continued by GPSR, SMJS and GJB at the EBI (European Bioinformatics Institute) with support from EMBL (European Molecular Biology Laboratory) to GJB and SMJS.  ... 
doi:10.1186/1471-2105-4-47 pmid:14552658 pmcid:PMC280650 fatcat:5lcp7bxjrbdc5lrpgdgldatdy4
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