Genomic Perl : from bioinformatics basics to working code /

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There are many basic computational problems in molecular biology and this text gives concise, working programs to solve them using Perl. With minimal prerequisites, the author explains the biological background for each problem, develops a model for the solution, then introduces the Perl concepts ne...

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Detalles Bibliográficos
Clasificación:Libro Electrónico
Autor principal: Dwyer, Rex A. (Autor)
Formato: Electrónico eBook
Idioma:Inglés
Publicado: Cambridge, UK ; New York : Cambridge University Press, 2003.
Temas:
Perl (Computer program language)
Molecular biology > Data processing.
Bioinformatics.
Programming languages (Electronic computers)
Computational biology.
Computational Biology
Genetics
Programming Languages
Perl (Langage de programmation)
Biologie moléculaire > Informatique.
Bio-informatique.
Langages de programmation.
COMPUTERS > Bioinformatics.
Computational biology
Bioinformatics
Molecular biology > Data processing
Molekulare Bioinformatik
Perl > Programmiersprache
Biologie moléculaire.
Acceso en línea:Texto completo
Tabla de Contenidos:
  • The Central Dogma
  • DNA and RNA
  • Chromosomes
  • Proteins
  • The Central Dogma
  • Transcription and Translation in Perl
  • RNA Secondary Structure
  • Messenger and Catalytic RNA
  • Levels of RNA Structure
  • Constraints on Secondary Structure
  • RNA Secondary Structures in Perl
  • Counting Hydrogen Bonds
  • Folding RNA
  • Comparing DNA Sequences
  • DNA Sequencing and Sequence Assembly
  • Alignments and Similarity
  • Alignment and Similarity in Perl
  • Predicting Species: Statistical Models
  • Perl Subroutine Libraries
  • Species Prediction in Perl
  • Substitution Matrices for Amino Acids
  • More on Homology
  • Deriving Substitution Matrices from Alignments
  • Substitution Matrices in Perl
  • The PAM Matrices
  • PAM Matrices in Perl
  • Sequence Databases
  • FASTA Format
  • GenBank Format
  • GenBank's Feature Locations
  • Reading Sequence Files in Perl
  • Object-Oriented Programming in Perl
  • The SimpleReader Class
  • Hiding File Formats with Method Inheritance
  • Local Alignment and the BLAST Heuristic
  • The Smith-Waterman Algorithm
  • The BLAST Heuristic
  • Preprocessing the Query String
  • Scanning the Target String
  • Implementing BLAST in Perl
  • Statistics of BLAST Database Searches
  • BLAST Scores for Random DNA
  • BLAST Scores for Random Residues
  • BLAST Statistics in Perl
  • Interpreting BLAST Output
  • Multiple Sequence Alignment I
  • Extending the Needleman-Wunsch Algorithm
  • NP-Completeness
  • Alignment Merging: A Building Block for Heuristics
  • Merging Alignments in Perl
  • Finding a Good Merge Order.

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