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Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures
2012
BMC Bioinformatics
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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
2011
Bioessays
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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
2006
BMC Bioinformatics
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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
2009
Computer applications in the biosciences : CABIOS
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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]
2005
Methods of biochemical analysis
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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
2011
PLoS ONE
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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
2007
BMC Bioinformatics
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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]
2002
Methods of biochemical analysis
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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
2014
Journal of Computational Biology
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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
2006
PLoS Genetics
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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
2016
Methods
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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
2009
BMC Genomics
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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
2014
International Journal of Bioinformatics Research and Applications
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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
2010
Nucleic Acids Research
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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
2003
BMC Bioinformatics
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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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