Managing your biological data with Python. ([2014])

• Record Type: Book
• Further Information: Note: Allegra Via, Kristian Rother, Anna Tramontano.
• Authors: Via, Allegra
• Other Names: Rother, Kristian; Tramontano, Anna
• Contents: Getting Started; The Python Shell; In This Chapter You Will Learn; Story: Calculating the ΔG of ATP Hydrolysis; What Do the Commands Mean?; Examples; Testing Yourself Your First Python Program; In This Chapter You Will Learn; Story: How to Calculate the Frequency of Amino Acids from Insulin; What Do the Commands Mean?; Examples; Testing Yourself Data Management; Analyzing a Data Column; In This Chapter You Will Learn; Story: Dendritic Lengths; What Do the Commands Mean?; Examples; Testing Yourself Parsing Data Records; In This Chapter You Will Learn; Story: Integrating Mass Spectrometry Data into Metabolic Pathways; What Do the Commands Mean?; Examples; Testing Yourself Searching Data ; In This Chapter You Will Learn; Story: Translating an RNA Sequence into the Corresponding Protein Sequence; What Do the Commands Mean?; Examples; Testing Yourself Filtering Data ; In This Chapter You Will Learn; Story: Working with RNA-Seq Output Data; What Do the Commands Mean?; Examples; Testing Yourself Managing Tabular Data ; In This Chapter You Will Learn; Story: Determining Protein Concentrations; What Do the Commands Mean?; Examples; Testing Yourself Sorting Data ; In This Chapter You Will Learn; Story: Sort a Data Table; What Do the Commands Mean?; Examples; Testing Yourself Pattern Matching and Text Mining ; In This Chapter You Will Learn; Story: Search a Phosphorylation Motif in a Protein Sequence; What Do the Commands Mean?; Examples; Testing Yourself Modular Programming; Divide a Program into Functions ; In This Chapter You Will Learn; Story: Working with Three-Dimensional Coordinate Files; What Do the Commands Mean?; Examples; Testing Yourself Managing Complexity with Classes ; In This Chapter You Will Learn; Story: Mendelian Inheritance; What Do the Commands Mean?; Examples; Testing Yourself Debugging ; In This Chapter You Will Learn; Story: When Your Program Does Not Work; What Do the Commands Mean?; Examples; Testing Yourself Using External Modules: The Python Interface to R ; In This Chapter You Will Learn; Story: Reading Numbers from a File and Calculating Their Mean Value Using R with Python; What Do the Commands Mean?; Examples; Testing Yourself Building Program Pipelines; In This Chapter You Will Learn; Story: Building an NGS Pipeline; What Do the Commands Mean?; Examples; Testing Yourself Writing Good Programs ; In This Chapter You Will Learn; Problem Description: Uncertainty; What Do the Commands Mean?; Examples; Testing Yourself Data Visualization; Creating Scientific Diagrams ; In This Chapter You Will Learn; Story: Nucleotide Frequencies in the Ribosome; What Do the Commands Mean?; Examples; Testing Yourself Creating Molecule Images with PyMOL ; In This Chapter You Will Learn; Story: The Zinc Finger; Seven Steps to Create a High-Resolution Image; Examples; Testing Yourself Manipulating Images ; In This Chapter You Will Learn; Story: Plot a Plasmid; What Do the Commands Mean?; Examples; Testing Yourself Biopython; Working with Sequence Data ; In This Chapter You Will Learn; Story: How to Translate a DNA Coding Sequence into the Corresponding Protein Sequence and Write It to a FASTA File; What Do the Commands Mean?; Examples; Testing Yourself Retrieving Data from Web Resources ; In This Chapter You Will Learn; Story: Searching Publications by Keywords in PubMed, Downloading the Corresponding Records, and Writing Papers Published in a Given Year to a File; What Do the Commands Mean?; Examples; Testing Yourself Working with 3D Structure Data ; In This Chapter You Will Learn; Story: Extracting Atom Names and Three-Dimensional Coordinates from a PDB File; What Do the Commands Mean?; Examples; Testing Yourself Cookbook; Recipe 1: The PyCogent Library; Recipe 2: Reversing and Randomizing a Sequence; Recipe 3: Creating a Random Sequence with Probabilities; Recipe 4: Parsing Multiple Sequence Alignments Using Biopython; Recipe 5: Calculating a Consensus Sequence from a Multiple Sequence Alignment; Recipe 6: Calculating the Distance between Phylogenetic Tree Nodes; Recipe 7: Codon Frequencies in a Nucleotide Sequence; Recipe 8: Parsing RNA 2D Structures in the Vienna Format; Recipe 9: Parsing BLAST XML Output; Recipe 10: Parsing SBML Files; Recipe 11: Running BLAST; Recipe 12: Accessing, Downloading, and Reading Web Pages in Python; Recipe 13: Parsing HTML Files; Recipe 14: Split a PDB File into PDB Chain Files; Recipe 15: Find the Two Closest Cα Atoms in a PDB Structure; Recipe 16: Extract the Interface between Two PDB Chains; Recipe 17: Building Homology Models Using Modeller; Recipe 18: RNA 3D Homology Modeling with ModeRNA; Recipe 19: Calculating RNA Base Pairs from a 3D Structure; Recipe 20: A Real Case of Structural Superimposition: The Serine Protease Catalytic Triad Appendix A: Command Overview; Appendix B: Python Resources; Appendix C: Record Samples; Appendix D: Handling Directories and Programs with UNIX
• Publisher Details: Boca Raton, FL : CRC Press
• Publication Date: 2014
• Copyright Date: 2014
• Extent: 1 online resource (xxvii, 524 pages), illustrations
• Subjects: 570.3; Biology -- Data processing; Python (Computer program language); Biology -- Data processing; Python (Computer program language); NATURE / Reference; SCIENCE / Life Sciences / Biology; SCIENCE / Life Sciences / General; Electronic books
• Languages: English
• ISBNs: 9781439880944; 1439880948
• Related ISBNs: 9781466540378; 1466540370; 1439880948; 143988093X; 1322612692; 9781322612690; 9781439880937
• Notes: Note: Includes bibliographical references and index.; Note: Print version record.
• Access Rights: Legal Deposit; Only available on premises controlled by the deposit library and to one user at any one time; The Legal Deposit Libraries (Non-Print Works) Regulations (UK).
• Access Usage: Restricted: Printing from this resource is governed by The Legal Deposit Libraries (Non-Print Works) Regulations (UK) and UK copyright law currently in force.