<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/991?offset=30 https://bioinformaticsonline.com/pages/view/36384/binding-site-prediction-in-protein Wed, 25 Apr 2018 04:35:57 -0500 https://bioinformaticsonline.com/pages/view/36384/binding-site-prediction-in-protein <![CDATA[Binding Site Prediction in Protein !]]> The interaction between proteins and other molecules is fundamental to all biological functions. In this section we include tools that can assist in prediction of interaction sites on protein surface and tools for predicting the structure of the intermolecular complex formed between two or more molecules (docking).

Pockets Identification

CASTp

Automatic Identification of pockets and cavities in proteins structure, and quantitation of their volumes using Delaunay triangulation. Available also as PyMOL plugin

Pocket-Finder

Automatic identification of pockets and cavities in proteins structure, and quantitation of their volumes.

PocketPicker

Grid-based technique for the analysis of protein pockets. PocketPicker available as a plugin for PyMOL
 

Binding Site Prediction

ConSurf

 
Identification of functional regions in proteins by surface-mapping of phylogenetic information
 
 
Identification protein interaction sites. It uses sequence conservation patterns in homologous proteins to distinguish between residues that are conserved due to structural restraints from those due to functional restraints.  
 
Ligand Binding Sites
 
 
The server utilizes protein-structure prediction to provide structural models of the binding site. Ligands bound to structures are superimposed onto the model and use to predict the binding site.
 
 
A threading-based method for ligand-binding site prediction and functional annotation based on binding-site similarity across superimposed groups of threading templates.
 

LIGSITEcsc

 
Prediction of binding site by pocket identification using the Connolly surface and degree of conservation

 
metaPocketA meta server for ligand-binding site prediction. metaPocket use LIGSITEcsc, PASS, Q-SiteFinder and SURFNET
]]> Poonam Mahapatra https://bioinformaticsonline.com/news/view/44604/new-release-of-refseq Tue, 16 Jul 2024 10:09:21 -0500 https://bioinformaticsonline.com/news/view/44604/new-release-of-refseq <![CDATA[New Release of RefSeq !]]> Check out RefSeq release 225, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.

What’s included in this release?

As of July 8, 2024, this full release incorporates genomic, transcript, and protein data containing:

  • 448,507,905 records
  • 334,845,613 proteins
  • 63,542,774 RNAs
  • Sequences from 152,668 organisms

The release is provided in several directories as a complete dataset and also as divided by logical groupings.

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/26539/scikit-learn Mon, 29 Feb 2016 17:39:24 -0600 https://bioinformaticsonline.com/bookmarks/view/26539/scikit-learn <![CDATA[scikit-learn]]> Machine Learning in Python

Simple and efficient tools for data mining and data analysis
Accessible to everybody, and reusable in various contexts
Built on NumPy, SciPy, and matplotlib
Open source, commercially usable - BSD license

More at http://scikit-learn.org/stable/index.html

 

Address of the bookmark: http://scikit-learn.org/stable/auto_examples/index.html

]]> Jitendra Prajapati https://bioinformaticsonline.com/pages/view/2261/best-book-titles-for-learning-bionformatics Tue, 13 Aug 2013 17:31:51 -0500 https://bioinformaticsonline.com/pages/view/2261/best-book-titles-for-learning-bionformatics <![CDATA[Best book Titles for Learning Bionformatics]]> Nothing can add to our intellect more than reading a book.  In books, we can experience new things that we would not normally be able to experience. It is proved that books can change our lives and other people’s lives. Reading can make us more intelligent, updated, imaginative. Without reading we wouldn’t know anything that we know today. There are several book, online and offile to read and I can't mentioned all of them here in the list. Therefore, I mentioned some bioinformatics and its related books in subgroups. Hope you will like the list. 

Sequence Analysis and General Bioinformatics

  • BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly
  • Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl Leon, 2003, O'Reilly
  • Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley & Sons
  • Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley & Sons
  • Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press
  • Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall
  • Evolutionary Computation in Bioinformatics, Gary B. Fogel, David W. Corne (Editors), 2002, Morgan Kaufmann
  • Introduction to Bioinformatics, Arthur M. Lesk, 2002, Oxford University Press
  • Instant Notes in Bioinformatics, D.R. Westhead, J. H. Parish, R.M. Twyman, 2002, Bios Scientific Pub
  • Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L. Raymer, Elaine Nicpon Marieb, 2002, Benjamin/Cummings
  • Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons
  • Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press
  • Hidden Markov Models for Bioinformatics, Timo Koski, Timo Koskinen, 2001, Kluwer Academic Publishers
  • Bioinformatics: From Genomes to Drugs, Thomas Lengauer (Editor), 2001, John Wiley & Sons
  • Statistical Methods in Bioinformatics: An Introduction (Statistics for Biology and Health), Warren Ewens, Gregory Grant, 2001, Springer Verlag
  • Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition, Andreas D. Baxevanis, B. F. Francis Ouellette, 2001, Wiley-Interscience
  • Bioinformatics: The Machine Learning Approach, Second Edition (Adaptive Computation and Machine Learning), Pierre Baldi, Soren Brunak, Sren Brunak, 2001, MIT Press
  • Introduction to Bioinformatics, T eresa Attwood, David Parry-Smith, 2001, Prentice Hall
  • Bioinformatics: A Primer, Charles Staben, 2001, Jones & Bartlett Pub
  • Data Analysis and Classification for Bioinformatics, Arun Jagota, 2000, AKJ Academics
  • Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor Laboratory Press
  • Bioinformatics: A Biologist's Guide to Biocomputing and the Internet, Stuart M. Brown, 2000, Eaton Pub Co
  • Bioinformatics: Sequence, Structure and Databanks: A Practical Approach (The Practical Approach Series, 236), Des Higgins (Editor), Willie Taylor (Editor), 2000, Oxford Univ Press
  • Neural Networks and Genome Informatics, Cathy H. Wu, Jerry W. McLarty, 2000, Elsevier Science
  • Computational Molecular Biology: An Introduction (Wiley Series in Mathematical and Computational Biology), Peter Clote and Rolf Backofen, 2000, John Wiley & Sons
  • Computational Molecular Biology: An Algorithmic Approach, Pavel A. Pevzner, 2000, MIT Press
  • Post-Genome Informatics, Minoru Kanehisa, 2000, Oxford Univ Press
  • Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity, and Digital Evolution, Chrystopher L. Nehaniv, 1999, American Mathematical Society
  • Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications, Jason T. L. Wang, Bruce A. Shapiro, Dennis Elliott Shasha (Editors), 1999, Oxford Univ Press
  • Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, David Sankoff and Joseph Kruskal (Editors), 1999, Cambridge University Press
  • Bioinformatics Basics: Applications in Biological Science and Medicine, Hooman Rashidi, 1999, CRC Press
  • Bioinformatics: Methods and Protocols (Methods in Molecular Biology, Vol 132), Stephen Misener and Stephen A. Krawetz (Editors),1999, Humana Press
  • Bioinformatics: Databases and Systems, Stanley Letovsky (Editor),1999, Kluwer Academic Publishers
  • Computational Molecular Biology, P. Green, 1998, Blackwell Science Inc.
  • Computational Methods in Molecular Biology (New Comprehensive Biochemistry, V. 32), Steven L. Salzberg, David B. Searls, Simon Kasif (Editors), 1998, Elsevier Science Ltd.
  • Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Richard Durbin, S. Eddy, A. Krogh, G. Mitchison, 1998, Cambridge University Press
  • Guide to Human Genome Computing, M. J. Bishop (Editor), 1998, Academic Press
  • Introduction to Computational Molecular Biology, Joao Meidanis, Joao C. Setabal, 1997, PWS Pub. Co.
  • Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Dan Gusfield, 1997, Cambridge University Press
  • Sequence Data Analysis Guidebook, Simon R. Swindell (Editor), 1997, Humana Press
  • High Performance Computational Methods for Biological Sequence Analysis, Tieng K. Yap, Ophir Frieder, Robert L. Martino, 1996, Kluwer Academic Pub.
  • Computer Methods for Macromolecular Sequence Analysis, Methods in Enzymology, volume 266, Russell F. Doolittle (Editor), 1996, Academic Press
  • DNA and Protein Sequence Analysis: A Practical Approach (Practical Approach Series , No 171), 1996, M. J. Bishop and C. J. Rawlings (Editors), 1996, IRL Press
  • Molecular Bioinformatics: Algorithms and Applications, Steffen Schulze-Kremer, 1995, Walter De Gruyter
  • Introduction to Computational Biology - Maps, sequences and genomes, Michael S. Waterman, 1995, Chapman & Hall
  • Computer Analysis of Sequence Data, Annette M. Griffin and Hugh G. Griffin (Editors), 1994, Humana Press
  • Artificial Intelligence and Molecular Biology, Lawrence Hunter (Editor), 1993, AAAI Press
  • Sequence Analysis Primer, Michael Gribskov and John Devereux (Editors), 1992, Oxford University Press
  • Mathematical Methods of Analysis of Biopolymer Sequences (Dimacs Series in Discrete Mathematics and Theoretical Computer Science ; Volume 8), S. G. Gindikin, 1992, American Mathematical Society
  • Mathematical Methods for DNA Sequences, Michael S. Waterman (Editor), 1989, CRC Press

Programming Books for Bioinformatics

  • Mastering Perl for Bioinformatics, James D. Tisdall, 2003, O'Reilly
  • Genomic Perl: From Bioinformatics Basics to Working Code, Rex A. Dwyer, 2002, Cambridge University Press
  • Beginning Perl for Bioinformatics, James Tisdall, 2001, O'Reilly
  • Developing Bioinformatics Computer Skills, Cynthia Gibas, Per Jambeck, 2001, O'Reilly

General Genomics

  • Functional Microbial Genomics (Volume 33), Brendan Wren, Nick Dorrell, 2003, Academic Press
  • Discovering Genomics, Proteomics, and Bioinformatics, A. Malcolm Campbell, Laurie J. Heyer, 2002, Benjamin/Cummings
  • Genomes, Terence A. Brown, 2002, John Wiley & Sons
  • Essentials of Medical Genomics, Stuart M. Brown , 2002, John Wiley & Sons
  • A Primer of Genome Science, Greg Gibson, Spencer V. Muse, 2002, Sinauer Associates
  • Pathogen Genomics: Impact on Human Health, Karen Joy, Phd Shaw (Editors), 2002, Humana Press
  • Genomics, John E. Antonopoulos, 2000, Xlibris Corporation
  • Genomics and Proteomics: Functional and Computational Aspects, Sandor Suhai (Editor), 2000, Plenum Pub Corp
  • Functional Genomics: A Practical Approach (The Practical Approach Series, 235), S. Hunt and F. Livesey (Editors), 2000, Oxford Univ Press
  • Human Molecular Genetics, Andrew P. Read, Tom Strachan 1999, BIOS Scientific Publishers Ltd.
  • Genomics: The Science and Technology Behind the Human Genome Project, Charles R. Cantor and Cassandra L. Smith, 1999, John Wiley & Sons
  • Cells: A Laboratory Manual, 3 volumes, David L. Spector, Robert D. Goldman, Leslie A. Leinwand, 1998, Cold Spring Harbor Laboratory Press
  • Genome Analysis: A Laboratory Manual, 4 volumes, Bruce Birren, et al. (Editors), 1997, Cold Spring Harbor Laboratory Press
  • The Human Genome Project, N. G. Cooper (Editor), 1994, University Science Books

Comparative Genomics

  • Handbook of Comparative Genomics: Principles and Methodology, Cecilia Saccone, Graziano Pesole, 2003, Wiley-Liss
  • Sequence - Evolution - Function: Computational Approaches in Comparative Genomics, Eugene V. Koonin, Michael Y. Galperin, 2002, Kluwer Academic Publishers
  • Comparative Genomics - Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, David Sankoff and Joseph H. Nadeau, 2000, Kluwer Academic Pub
  • Comparative Genomics, Melody Clark (Editor), 2000, Kluwer Academic Pub

Proteomics

  • Proteins and Proteomics: A Laboratory Manual, Richard J. Simpson (Editor), Cold Spring Harbor Laboratory
  • Proteomics in Practice: A Laboratory Manual of Proteome Analysis , Reiner Westermeier, Tom Naven, 2002, John Wiley & Sons
  • Posttranslational Modifications of Proteins: Tools for Functional Proteomics (Methods in Molecular Biology, Vol 194) , Christoph Kannicht (Editor), 2002, Humana Press
  • Peptide Arrays on Membrane Supports: Synthesis and Applications (Springer Lab Manual), Joachim Koch, Michael Mahler (Editors), 2002, Springer Verlag
  • Proteomics , Timothy Palzkill, 2002, Kluwer Academic Publishers
  • Introduction to Proteomics: Tools for the New Biology , Daniel C. Liebler (Editor), 2001, Humana Press
  • Proteome Research: Mass Spectrometry (Principles and Practice) , P. James (Editor), 2001, Springer Verlag
  • Interpreting Protein Mass Spectra: A Comprehensive Resource , A. Peter Snyder, 2000, American Chemical Society
  • Protein Sequencing and Identification Using Tandem Mass Spectrometry , Michael Kinter, Nicholas E. Sherman, 2000, Wiley-Interscience
  • From Genome to Proteome: Advances in the Practice and Application of Proteomics, Michael J. Dunn (Editor), 2000, Vch Verlagsgesellschaft Mbh
  • Proteomics: From Protein Sequence to Function, S. Pennington (Editor), M. Dunn (Editor), 2000, Springer Verlag
  • Proteome Research: Two-Dimensional Gel Electrophoresis and Detection Methods (Principles and Practice), T. Rabilloud (Editor), 2000, Springer Verlag
  • Proteome and Protein Analysis, R. M. Kamp, D. Kyriakidis, th Choli-Papadopoulou (Editor), 1999, Springer Verlag
  • Proteome Research: New Frontiers in Functional Genomics, M. R. Wilkins, et al. (Editors), 1997, Springer Verlag

Protein Structure

  • Structural Bioinformatics, Philip E. Bourne, Helge Weissig (Editors), 2003, John Wiley & Sons
  • Protein Structure Prediction: Bioinfomatic Approach, I.F. Tsigelny, 2002, International University Line
  • Introduction to Protein Architecture: The Structural Biology of Proteins, Arthur M. Lesk, 2001, Oxford University Press
  • Protein Structure Prediction: Methods and Protocols, David M. Webster (Editor), 2000, Humana Press
  • Introduction to Protein Structure, Carl-Ivar Branden, John Tooze, 1999, Garland Publishing
  • Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Alan Fersht, 1999, Freeman

Pharmacogenomics

  • Pharmacogenomics: Social, Ethical, and Clinical Dimensions, Mark A. Rothstein (Editor), 2003, Wiley-Liss
  • Pharmacogenomics: The Search for Individualized Therapies, Julio Licinio, Ma-Li Wong (Editors), 2002, John Wiley & Sons
  • Pharmacogenomics, Werner Kalow, Urs A. Meyer, Rachel Tyndale (Editors), 2001, Marcel Dekker
  • Pharmacogenetics and Pharmcogenomics: Recent Conceptual and Technical Advances (Pharmacology, Volume 61, Number 3, 2000), Elliot S. Vesell (Editor), 2000, S. Karger Publishing
  • Pharmacogenetics, Wendell Weber, 1997, Oxford University Press

DNA Microarrays

  • Statistical Analysis of Gene Expression Microarray Data, T. P. Speed (Editor), 2003, CRC Press
  • Microarray Gene Expression Data Analysis: A Beginner's Guide, Helen C. Causton, John Quackenbush, Alvis Brazma, 2003, Blackwell Publishers
  • The Analysis of Gene Expression Data (Statistics for Biology and Health), G. Parmigiani, E. S. Garrett, R. A. Irizarry, S. Zeger , Graeme Clark (Editors), 2003, Springer Verlag
  • A Practical Approach to Microarray Data Analysis, Daniel P. Berrar, Werner Dubitzky, Martin Granzow (Editors), 2002, Kluwer Academic Publishers
  • DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling, Pierre Baldi, G. Wesley Hatfield, 2002, Cambridge University Press
  • DNA Microarrays: A Molecular Cloning Manual, David Bowtell, Joseph Sambrook (Editors), 2002, Cold Spring Harbor Laboratory
  • DNA Array Image Analysis: Nuts & Bolts, Gerda Kamberova, Shishir Shah, 2002, DNA Press
  • Microarray Analysis, Mark Schena, 2002, John Wiley & Sons
  • A Biologist's Guide to Analysis of DNA Microarray Data, Steen Knudsen, 2002, John Wiley & Sons
  • Microarrays for an Integrative Genomics (Computational Molecular Biology), Isaac S. Kohane, Alvin Kho, Atul J. Butte, 2002, MIT Press
  • Microarrays for the Neurosciences: An Essential Guide (Cellular and Molecular Neuroscience), Daniel H. Geschwind, Jeffrey P. Gregg (Editors), 2002, MIT Press
  • DNA Microarrays: Gene Expression Applications, Bertrand Jordan (Editor), 2001, Springer Verlag
  • DNA Arrays: Methods and Protocols (Methods in Molecular Biology, Volume 170), Jang B. Rampal (Editor), 2001, Humana Press
  • DNA Arrays: Technologies and Experimental Strategies, Elena V. Grigorenko (Editor), 2001, CRC Press
  • Microarray Biochip Technology, Mark Schena (Editor), 2000, Eaton Pub
  • Expression Genetics: Accelerated and High-Throughput Methods (Biotechniques Update Series), Michael McClelland (Editor), Arthur B. Pardee (Editor), 1999, Eaton Pub
  • DNA Microarrays: A Practical Approach (Practical Approach Series 205), Mark Schena (Editor), 1999, Oxford Univ Press
  • cDNA Preparation and Characterization (Methods in Enzymology Volume 303), S.M. Weissman (Editor), 1999, Academic Press

Systems Biology, Genetic and Biochemical Network

  • Handbook of Graphs and Networks : From the Genome to the Internet, Stefan Bornholdt, Heinz Georg Schuster (Editors), 2003, Vch Verlagsgesellschaft Mbh
  • Computational Cell Biology, Christopher Fall, Eric Marland, John Wagner, John Tyson (Editors), 2002, Springer Verlag
  • Gene Regulation and Metabolism: Post-Genomic Computational Approaches (Computational Molecular Biology), Julio Collado-Vides, Ralf Hofestadt (Editors), 2002, MIT Press
  • Foundations of Systems Biology, Hiroaki Kitano (Editor), 2001, MIT Press
  • Genomic Regulatory Systems: Development and Evolution, Eric H. Davidson , 2001, Academic Press
  • Genes & Signals, Mark Ptashne, Alexander Gann, 2001, Cold Spring Harbor Laboratory
  • Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology), James M. Bower and Hamid Bolouri (Editors), 2001, MIT Press
  • Protein-Protein Interactions: A Molecular Cloning Manual, Erica Golemis (Editor), 2001, Cold Spring Harbor Laboratory
  • Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists, Eberhard O. Voit, 2000, Cambridge University Press
  • Mathematical Physiology, James P. Keener, James Sneyd, 1998, Springer Verlag

 

DNA Sequencing

  • DNA Sequencing: From Experimental Methods to Bioinformatics (Introduction to Biotechniques Series), Luke Alphey, 1997, Springer Verlag
  • Automated DNA sequencing and analysis, Adams M.D., Fields C., Venter J.C. (Editors), 1994, Academic Press

 

Apart from above mentioned books, you can also find some useful books links at following mentioned URLs:

 

http://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713

http://www.amazon.com/Bioinformatics-Genes-Proteins-Computers-Advanced/dp/1859960545

http://www.amazon.com/Introduction-Bioinformatics-Algorithms-Computational-Molecular/dp/0262101068

http://books.google.no/books?id=pxSM7R1sdeQC&dq=Pierre+baldi+%2B+bioinformatics&printsec=frontcover&source=bn&hl=en&ei=IoGRS6uCIJT-NYLA8Z0N&sa=X&oi=book_result&ct=result&redir_esc=y#v=onepage&q&f=false

http://www.amazon.com/Statistical-Methods-Bioinformatics-Introduction-Statistics/dp/0387400826

 

If you think your favourite books are not listed then please write it down in comment section for the benefits of other users. Feel free to add many more books in comment section. 

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/44252/orange-data-mining Mon, 13 Mar 2023 12:42:29 -0500 https://bioinformaticsonline.com/bookmarks/view/44252/orange-data-mining <![CDATA[Orange: Data mining]]>

Open source machine learning and data visualization.

Build data analysis workflows visually, with a large, diverse toolbox.

 

Address of the bookmark: https://orangedatamining.com/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture Fri, 27 Sep 2013 04:24:45 -0500 https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture <![CDATA[Molecular Genetics Lecture]]> "Robert Sapolsky makes interdisciplinary connections between behavioral biology and molecular genetic influences. He relates protein synthesis and point mutations to microevolutionary change, and discusses conflicting theories of gradualism and punctuated equilibrium and the influence of epigenetics on development theories." 

"Robert Sapolsky is an American neuroendocrinologist, professor of biology, neuroscience, and neurosurgery at Stanford University, researcher and author" ----Wikipedia

Address of the bookmark: http://www.youtube.com/watch?v=_dRXA1_e30o

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/36752/minmax-a-versatile-tool-for-calculating-and-comparing-synonymous-codon-usage-and-its-impact-on-protein-folding Thu, 24 May 2018 02:53:31 -0500 https://bioinformaticsonline.com/bookmarks/view/36752/minmax-a-versatile-tool-for-calculating-and-comparing-synonymous-codon-usage-and-its-impact-on-protein-folding <![CDATA[%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.]]> Address of the bookmark: http://www.codons.org/

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/37965/kobas-a-web-server-for-geneprotein-functional-annotation-and-functional-gene-set-enrichment Fri, 19 Oct 2018 09:36:11 -0500 https://bioinformaticsonline.com/bookmarks/view/37965/kobas-a-web-server-for-geneprotein-functional-annotation-and-functional-gene-set-enrichment <![CDATA[KOBAS: a web server for gene/protein functional annotation and functional gene set enrichment]]> KOBAS 3.0 is a web server for gene/protein functional annotation (Annotate module) and functional gene set enrichment(Enrichment module). For Annotate module, it accepts gene list as input, including IDs or sequences, and generates annotations for each gene based on multiple databases about pathways, diseases, and Gene Ontology. For Enrichment module, it can accept either gene list or gene expression data as input, and generates enriched gene sets, corresponding name, p-value or a probability of enrichment and enrichment score based on results of multiple methods.

Address of the bookmark: http://kobas.cbi.pku.edu.cn/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42405/caretta-%E2%80%93-a-multiple-protein-structure-alignment-and-feature-extraction-suite Fri, 18 Dec 2020 02:09:44 -0600 https://bioinformaticsonline.com/bookmarks/view/42405/caretta-%E2%80%93-a-multiple-protein-structure-alignment-and-feature-extraction-suite <![CDATA[Caretta – A multiple protein structure alignment and feature extraction suite]]> Caretta – a multiple protein structure alignment and feature extraction suite

Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments with a higher coverage than current state-of-the-art tools. Caretta is available as a GUI and command-line application and additionally outputs an aligned structure feature matrix for a given set of input structures, which can readily be used in downstream steps for supervised or unsupervised machine learning. 

Address of the bookmark: http://www.bioinformatics.nl/caretta/

]]> Rahul Nayak https://bioinformaticsonline.com/researchlabs/view/4546/sowdhamini-lab Sun, 15 Sep 2013 09:19:12 -0500 <![CDATA[SOWDHAMINI Lab]]> Genome sequencing projects have enormous potential for benefiting human endeavors. However, just as acquiring a language's vocabulary does not enable one to speak it, databases that list the amino acid composition of proteins do not directly tell us much about these proteins' higher-level structure and function. The most productive way to indirectly exploit these databases has been to start with the small number of proteins that are fully-characterised and to assume that other "similar" proteins will have a related structure and function. Proteins with very similar amino acid sequence are "no-brainers", but the real test, which our group largely focuses on, is to detect the "essential" similarity in proteins whose non-critical sections have experienced random rearrangements during evolution. In such cases functionally similar proteins may have less than 25% sequence overlap.

More @ http://www.ncbs.res.in/sowdhamini/groups_sowdhamini.htm

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