Applying motif and profile searches.

Keywords

Motif (music), Computer science, Sequence homology, Sequence motif, Homology (biology)

References

• Automated assembly of protein blocks for database searching.一男 宮川, 勇 市嶋, 誠一 渡辺 — 1991
• JAK3: a novel JAK kinase associated with terminal differentiation of hematopoietic cells.Sushil G. Rane, E. P. Reddy — 1994
• Yeast chromosome III: new gene functions.Eugene V. Koonin, Peer Bork, Chris Sander — 1994
• JAK2, a third member of the JAK family of protein tyrosine kinases.Ailsa G. Harpur, A.‐C. Andres, Andrew Ziemiecki — 1992
• Flexible protein sequence patterns. A sensitive method to detect weak structural similarities.Geoffrey J. Barton, Michael J.E. Sternberg — 1990
• Improving the sensitivity of the sequence profile methodRoland Lüthy, Ioannis Xénarios, Philipp Bücher — 1994
• Amino acid substitution during functionally constrained divergent evolution of protein sequences.S. A. Bennet, Mark A. Cohen, Gastón H. Gonnet — 1994
• Prediction of protein secondary structure at better than 70% accuracy.Burkhard Rost, Chris Sander — 1993
• Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiologyPeer Bork, Christos Ouzounis, Georg Casari — 1995
• The PH domain: a common piece in the structural patchwork of signalling proteins.Andrea Musacchio, Toby J. Gibson, Peter Rice — 1993
• Pattern matching methods in protein sequence comparison and structure prediction.William R. Taylor — 1988
• A Flexible Motif Search Technique Based on Generalized ProfilesPhilipp Bücher, Kevin Karplus, Nicolas Moeri — 1996
• Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.Charles E. Lawrence, Stephen F. Altschul, Mark S. Boguski — 1993
• DHR domains in syntrophins, neuronal NO synthases and other intracellular proteins.Chris P. Ponting, Christopher Phillips — 1995
• Issues in searching molecular sequence databasesStephen F. Altschul, Mark S. Boguski, Warren Gish — 1994
• The PHD finger: implications for chromatin-mediated transcriptional regulation.Rein Aasland — 1995
• A template based method of pattern matching in protein sequences.William R. Taylor — 1989
• A comprehensive set of sequence analysis programs for the VAXJohn Devereux, Paul Haeberli, Oliver Smithies — 1984
• Recognition of distantly related protein sequences using conserved motifs and neural networks.Dmitrij Frishman, Patrick Argos — 1992
• PH domain: the first anniversary.Toby J. Gibson, Marko Hyvönen, Andrea Musacchio — 1994

Cited by

• Extracting protein alignment models from the sequence database.Thomas DeGrand, B. Petersson — 1997
• Comparison of ARM and HEAT protein repeats.F.C.C. Liu, Denis M. Medeiros — 2001
• Sequence and structural links between distant ADP-ribosyltransferase families.J. Fernando Bazán, Friedrich Koch‐Nolte — 1997
• Janus Kinases and Focal Adhesion Kinases Play in the 4.1 Band: A Superfamily of Band 4.1 Domains Important for Cell Structure and Signal TransductionJean‐Antoine Girault, Gilles Labesse, J.-P. Mornon — 1998
• The identification of differentially expressed genes in sugarcane following infection with Fiji disease fijivirus.Judith M. Candy, BJ Croft, Stevens M. Brumbley — 2001
• Purification, crystallisation and X-ray structure analysis of proteins from the lysine biosynthetic pathway of Mycobacterium tuberculosis and structural studies of membrane proteins from Deinococcus radiodurans R1 and Escherichia coli K12Simone Weyand — 2007
• Pedestrian guide to analyzing sequence databasesBurkhard Rost, Reinhard Schneider, Chris Sander — 1997
• Protein Local Tertiary Structure Prediction by Super Granule Support Vector Machines with Chou-Fasman ParameterBernard Chen, Minwoo Kim, Matthew E. Johnson — 2012
• Sources of Systematic Error in Functional Annotation of Genomes: Domain Rearrangement, Non-Orthologous Gene Displacement and Operon DisruptionMichael Y. Galperin, Eugene V. Koonin — 1998
• Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanusGaudermann Peter, Ina Vogl, Evelyn Zientz — 2006
• Mathematically Complete Nucleotide and Protein Sequence Searching Using SsearchAlexander J. Ropelewski, Hugh B. Nicholas, David W. Deerfield — 2003
• More than 1,000 putative new human signalling proteins revealed by EST data miningJörg Schultz, Tobias Doerks, Chris P. Ponting — 2000
• Gene families: the taxonomy of protein paralogs and chimeras.Steven Henikoff, Elizabeth A. Greene, Shmuel Pietrokovski — 1997
• Detection of DNA-binding helix-turn-helix motifs in proteins using the pattern dictionary method.Kalai Mathee, Giri Narasimhan — 2003
• Extraction of Protein Sequence Motifs Information by Bi-Clustering AlgorithmVincent Yip, Bernard Chen, Sinan Kockara — 2010
• A superfamily of conserved domains in DNA damage‐ responsive cell cycle checkpoint proteinsPeer Bork, Kay Hofmann, Philipp Bücher — 1997
• Evolution of domain families.Chris P. Ponting, Jörg Schultz, Richard R. Copley — 2000
• Protein Structure Prediction using Coarse Grain Force FieldsNasir Mahmood — 2010
• Towards protein function annotations for matching remote homologsSeak Fei Lei — 2008
• dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarityWing‐Cheong Wong, Choon-Kong Yap, Birgit Eisenhaber — 2015

Related papers

• How does DNA sequence motif discovery work?Patrik D’haeseleer — 2006
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• Sequence of the cysteine peptides from the chicken 7·8S Ig heavy chain C-region. A comparison with the gamma chain of humansJames C. Travis, Bob G. Sanders — 1975
• Degrading Characters of a Degrading-Prometryn Strain and Amplification & Homology Analysis of the Degrading-Gene Conservative SequenceHui Yan — 2002
• ARCS-Motif: discovering correlated motifs from unaligned biological sequencesShijie Zhang, Wei Su, Jiong Yang — 2009
• U Subtle motifs: defining the limits of motif finding algorithmsUri Keich, Pavel A. Pevzner — 2002
• Quantifying similarity between motifsShobhit Gupta, J Stamatoyannopoulos, Timothy L. Bailey — 2007
• RPPMD (Randomly projected possible motif discovery): An efficient bucketing method for finding DNA planted MotifFaisal Bin Ashraf, Ali Imam Abir, Md Sirajus Salekin — 2017
• Sequencing and Analysis of Genome of Local Epidemic PCV-2 StrainsFang Liu — 2006