morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring
暂无分享,去创建一个
Jose M. Villaveces | Bianca Habermann | Malvika Sharan | Felix Oswald | Vineeth Surendranath | Michael Volkmer | Ines Wagner | B. Habermann | V. Surendranath | M. Sharan | J. Villaveces | F. Oswald | Michael Volkmer | I. Wagner
[1] P. Bonacich. Factoring and weighting approaches to status scores and clique identification , 1972 .
[2] Bianca Habermann,et al. Swm1/Apc13 Is an Evolutionarily Conserved Subunit of the Anaphase-Promoting Complex Stabilizing the Association of Cdc16 and Cdc27 , 2004, Molecular and Cellular Biology.
[3] Kimmen Sjölander,et al. The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification , 2013, Nucleic Acids Res..
[4] Kimmen Sjölander,et al. Berkeley PHOG: PhyloFacts orthology group prediction web server , 2009, Nucleic Acids Res..
[5] Salvador Capella-Gutiérrez,et al. PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions , 2010, Nucleic Acids Res..
[6] Trey Ideker,et al. Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..
[7] Erik L. L. Sonnhammer,et al. Inparanoid: a comprehensive database of eukaryotic orthologs , 2004, Nucleic Acids Res..
[8] E. Koonin,et al. Functional and evolutionary implications of gene orthology , 2013, Nature Reviews Genetics.
[9] A. Biegert,et al. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.
[10] D. Haussler,et al. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. , 1998, Journal of molecular biology.
[11] C. Stoeckert,et al. OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.
[12] David Haussler,et al. The UCSC genome browser database: update 2007 , 2006, Nucleic Acids Res..
[13] Maricel G Kann,et al. Performance evaluation of a new algorithm for the detection of remote homologs with sequence comparison , 2002, Proteins.
[14] Mary Goldman,et al. The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..
[15] Darren A. Natale,et al. The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.
[16] Albert J. Vilella,et al. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. , 2009, Genome research.
[17] Erik L. L. Sonnhammer,et al. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis , 2009, Nucleic Acids Res..
[18] D. P. Wall,et al. Detecting putative orthologs , 2003, Bioinform..
[19] Gautier Koscielny,et al. Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species , 2011, Nucleic Acids Res..
[20] M Kann,et al. Optimization of a new score function for the detection of remote homologs , 2000, Proteins.
[21] Thomas D. Cuypers,et al. Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase , 2012, Genome Biology.
[22] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[23] S. Eddy. Hidden Markov models. , 1996, Current opinion in structural biology.
[24] M. Ruggero,et al. Similarity of Traveling-Wave Delays in the Hearing Organs of Humans and Other Tetrapods , 2007, Journal for the Association for Research in Otolaryngology.
[25] W. Fitch. Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.
[26] Christian von Mering,et al. eggNOG: automated construction and annotation of orthologous groups of genes , 2007, Nucleic Acids Res..
[27] M. Sternberg,et al. Benchmarking PSI-BLAST in genome annotation. , 1999, Journal of molecular biology.
[28] Aric Hagberg,et al. Exploring Network Structure, Dynamics, and Function using NetworkX , 2008, Proceedings of the Python in Science Conference.
[29] Johannes Söding,et al. HHsenser: exhaustive transitive profile search using HMM–HMM comparison , 2006, Nucleic Acids Res..
[30] Frances M. G. Pearl,et al. The CATH extended protein‐family database: Providing structural annotations for genome sequences , 2002, Protein science : a publication of the Protein Society.