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Bioinformatics Resources
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  • Text/Documents:
     
    • What is Bioinformatics? (2001) (PDF, 487KB, 13pgs)
      N.M.Luscombe, D.Greenbaum, and M.Gerstein, provided by the Dept. of Molecular Biophysics and Biochemistry, Yale University
           The recent flood of data from genome sequences and functional genomics has given rise to a new field, bioinformatics, which combines elements of biology and computer science. The authors propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems. Bioinformatics is conceptualizing biology in terms of macromolecules and then applying "informatics" techniques (derived from applied mathematics, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale.
       
    • Molecular Biology for Computer Scientists (1993) (PDF, 192KB, 46pgs)
      By Lawrence Hunter, Chapter 1 from Artificial Intelligence and Molecular Biology (pp. 1-46)
            One of the major challenges for computer scientists who wish to work in the domain of molecular biology is becoming conversant with the daunting intricacies of existing biological knowledge and its extensive technical vocabulary. Questions about the origin, function, and structure of living systems have been pursued by nearly all cultures throughout history, and the work of the last two generations has been particularly fruitful. The knowledge of living systems resulting from this research is far too detailed and complex for any one human to comprehend...
       
    • DNA Microarray Data Analysis, second edition (2006) (Full Text avaliable at website)
      From CSC - the Finnish IT center for science
            This guidebook is written in collaboration between several Finnish researchers from different universities and research institutions. The first edition of the DNA microarray data analysis guidebook was written by M. Minna Laine, Tomi Pasanen, Janna Saarela, Ilana Saarikko, Teemu Toivanen, Martti Tolvanen, Jarno Tuimala, Mauno Vihinen, and Garry Wong. For the second edition, Iiris Hovatta, Katja Kimppa, Antti Lehmussola, Juha Saharinen, and Pekka Tiikkainen joined the writer team. The purpose of this book is to serve as course and teaching material to introduce basic concepts of microarray data analysis. We hope that especially researchers starting their data analysis can benefit from the book.
      Example chapters:
      Part II, Section 10: Data normalization
      Part II, Section 11: Finding differentially expressed genes
       
    • Finding the evidence for protein-protein interactions from PubMed abstracts (2006) (PDF, 442KB, 7pgs)
      Jang et al., Bioinformatics Team, Electronics and Telecommunications Research Institute (ETRI) in Korea
            As a result of a search for two proteins, PubMed frequently returns hundreds of abstracts. In this paper, a method is introduced that validates protein-protein interactions from PubMed abstracts.
       
    • Inferring protein domain interactions from databases of interacting proteins (2005) (Online Version)
      Riley et al., University of California at Los Angeles
            We describe domain pair exclusion analysis (DPEA), a method for inferring domain interactions from databases of interacting proteins. DPEA features a log odds score, Eij, reflecting confidence that domains i and j interact. We analyzed 177,233 potential domain interactions underlying 26,032 protein interactions. In total, 3,005 high-confidence domain interactions were inferred, and were evaluated using known domain interactions in the Protein Data Bank. DPEA may prove useful in guiding experiment-based discovery of previously unrecognized domain interactions.
       
    • In Silico Two-Hybrid System for the Selection of Physically Interacting Protein Pairs (2002) (PDF, 261KB, 9pgs)
      Florencio Pazos and Alfonso Valencia, CNB-CSIC, Madrid, Spain
            On the basis of the study of correlated mutations in multiple sequence alignments, we propose a new method (in silico twohybrid, i2h) that directly addresses the detection of physically interacting protein pairs and identifies the most likely sequence regions involved in the interactions. We have applied the systemto several test sets, showing that it can discriminate between true and false interactions in a significant number of cases.
       
    • GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data (2003) (PDF, 426KB, 11pgs)
      Rzhetsky et al., Columbia University, New York
            The immense growth in the volume of research literature and experimental data in the field of molecular biology calls for efficient automatic methods to capture and store information. In recent years, several groups have worked on specific problems in this area, such as automated selection of articles pertinent to molecular biology, or automated extraction of information using natural-language processing, information visualization, and generation of specialized knowledge bases for molecular biology. GeneWays is an integrated system that combines several such subtasks. It analyzes interactions between molecular substances, drawing on multiple sources of information to infer a consensus view of molecular networks. GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information.
       
    • What is a DNA chip? (2002) (PDF, 1,024KB, 11pgs)
      written for students by Russ Hodge and Christian Schwager, European Molecular Biology Laboratory (EMBL)
            This presentation introduces DNA chips (w/photos of real chips after an experiment), followed by DNA chip analysis software, explaining the meaning of spots seen on the chips. The article then explains DNA chip score charts and correlation graphs through an example in which a healthy and an infected mosquito are compared.
       
    • News Article: "Structure-based Drug Design" (June 4, 2001)
      Chemical & Engineering News
            The article points out and describes the (docking and cystallographic) methods employed and highlights the importance of structure-based design as a shortcut to find better compounds for new drugs. For more information about the company cited, logon to: www.syrrx.com
       
    • Webpage: "How is drug design related to bioinformatics?" (Date unkn.) (in English/German/French)
      Wolfram Altenhofen, University of Bielefeld, Germany
            Well designed webpage with comprehensive graphics (3D molecular models of proteins). Topics covered: A) Proteins as Cellular Targets of Medical Drugs, B) The Molecular Basis of Drug Specificity, C) "Rational" Drug Design, D) Techniques Applied, E) Drug Design Using Known Receptor Structures, F) What if we don't Know the Structure of the Receptor?, and G) Future Perspectives.
       
    • PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways (2006) (Online version)
      Maltsev et al., Argonne National Laboratory
            The PUMA2 system (available at http://compbio.mcs.anl.gov/puma2) is an interactive, integrated bioinformatics environment for high-throughput genetic sequence analysis and metabolic reconstructions from sequence data. PUMA2 provides a framework for comparative and evolutionary analysis of genomic data and metabolic networks in the context of taxonomic and phenotypic information. Grid infrastructure is used to perform computationally intensive tasks.
       
    • The COG database: an updated version includes eukaryotes (2003) (Online version)
      Tatusov et al., NIH, Bethesda, Maryland.
            We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups.
       
    • Article: "The Sequence of the Human Genome" (2001) (Online version)
      J. Craig Venter et al. (Science, 16 February 2001)
            A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies--a whole-genome assembly and a regional chromosome assembly--were used, each combining sequence data from Celera and the publicly funded genome effort...
       
    • Book Suggestions:
       
      • Beginning Perl for Bioinformatics
        by James Tisdall
        ISBN: 0596000804
        October 15, 2001
        400 pages
         
        A good introduction to the applications of Perl in Bioinformatics for students coming from a life sciences, rather than a computer science, background. Perl has relevance in areas like sequence analysis because it was originally developed to handle and manipulate text. As a result, it has variety of built-in regular expressions making text searching and manipulation fairly straightforward. This text displays uses of Perl that are immediately useful to a student of Bioinformatics; each chapter focuses on solving a particular bioinformatics problem or type of problem, with each chapter becoming more complex as your competence builds. See a related lecture by Stuart M. Brown.
         
         
  • Software Downloads:
     
    • EBI Bioinformatic Tools
      A collection of software provided by the European Bioinformatics Institute.
       
    • Swiss-PdbViewer
      For viewing proteins and molecules (as PDB files) in 3D. Download includes instruction manual.
       
    • Getting BioPerl
      Wiki directing you to the latest release of BioPerl
       
    • EMBOSS
      A free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Please see the documentation for the capabilities of EMBOSS, including this helpful guide to EMBOSS and other bioinformatics tools by Lisa Mullan of the EBI.
       
    • BioExchange - Bioinformatics Software Downloads
      Requires free account setup to download.
       
  • Slide Presentations:
     
  • Video Lectures:
     
  • Sample Scripts:
     
  • Sample Data:
     
    • Bacterial Genomes - Search through the genomes (avaliable as TXT files) of 331 (as of 08-07-06) bacterial microorganisms. Made available by the EMBL-EBI.
       
    • Genome Browser FTP server - Bulk downloads of sequences and annotation data made (most data is in compressed form) available via the Genome Browser FTP server.
       
  • General Web Resources:
     
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This page was created on September 23, 2009.