MDAT- Aligning multiple domain arrangements

[1]  Erich Bornberg-Bauer,et al.  Rapid similarity search of proteins using alignments of domain arrangements , 2014, Bioinform..

[2]  Alexandros Stamatakis,et al.  A daily-updated tree of (sequenced) life as a reference for genome research , 2013, Scientific Reports.

[3]  Erich Bornberg-Bauer,et al.  Dynamics and adaptive benefits of modular protein evolution. , 2013, Current opinion in structural biology.

[4]  Burkhard Morgenstern,et al.  DIALIGN at GOBICS—multiple sequence alignment using various sources of external information , 2013, Nucleic Acids Res..

[5]  F. Rentzsch,et al.  Repeated Evolution of Identical Domain Architecture in Metazoan Netrin Domain-Containing Proteins , 2012, Genome biology and evolution.

[6]  Caroline O. Buckee,et al.  Evolution of the Multi-Domain Structures of Virulence Genes in the Human Malaria Parasite, Plasmodium falciparum , 2012, PLoS Comput. Biol..

[7]  Erich Bornberg-Bauer,et al.  Dynamics and Adaptive Benefits of Protein Domain Emergence and Arrangements during Plant Genome Evolution , 2012, Genome biology and evolution.

[8]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[9]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[10]  M. Petz,et al.  La enhances IRES-mediated translation of laminin B1 during malignant epithelial to mesenchymal transition , 2011, Nucleic acids research.

[11]  Sarah A Teichmann,et al.  How do proteins gain new domains? , 2010, Genome Biology.

[12]  M. Levitt.  Nature of the protein universe , 2009, Proceedings of the National Academy of Sciences.

[13]  Minoru Kanehisa,et al.  Domain shuffling and the evolution of vertebrates. , 2009, Genome research.

[14]  Benedict Paten,et al.  Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment , 2009, Bioinform..

[15]  Andrew D. Moore,et al.  Arrangements in the modular evolution of proteins. , 2008, Trends in biochemical sciences.

[16]  Andrew E. Firth,et al.  GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries , 2008, Nucleic Acids Res..

[17]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[18]  Richa Agarwala,et al.  COBALT: constraint-based alignment tool for multiple protein sequences , 2007, Bioinform..

[19]  Robert D. Finn,et al.  Pfam: clans, web tools and services , 2005, Nucleic Acids Res..

[20]  Olivier Poch,et al.  BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark , 2005, Proteins.

[21]  L. Holm,et al.  The Pfam protein families database , 2011, Nucleic Acids Res..

[22]  Johannes Söding,et al.  Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..

[23]  A. Elofsson,et al.  Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. , 2005, Journal of molecular biology.

[24]  K. Katoh,et al.  MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.

[25]  Colin Berry,et al.  Structure, diversity, and evolution of protein toxins from spore-forming entomopathogenic bacteria. , 2003, Annual review of genetics.

[26]  S. Bryant,et al.  CDART: protein homology by domain architecture. , 2002, Genome research.

[27]  D. Higgins,et al.  T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.

[28]  O. Gotoh.  Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. , 1996, Journal of molecular biology.

[29]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[30]  D. Higgins,et al.  See Blockindiscussions, Blockinstats, Blockinand Blockinauthor Blockinprofiles Blockinfor Blockinthis Blockinpublication Clustal: Blockina Blockinpackage Blockinfor Blockinperforming Multiple Blockinsequence Blockinalignment Blockinon Blockina Minicomputer Article Blockin Blockinin Blockin , 2022 .

[31]  E. Sonnhammer,et al.  Evolution of protein domain architectures. , 2012, Methods in molecular biology.

[32]  M. O. Dayhoff.  A model of evolutionary change in protein , 1978 .

[33]  M. O. Dayhoff,et al.  22 A Model of Evolutionary Change in Proteins , 1978 .