Resources for Bioinformatics

Essential Information | For Further Reading | Other Links

About This Page

This page is a guide and collection of resources for Biology 325 at DePauw University. The number of resources available to the bioinformatician is overwhelming. Navigating these resources can be daunting and discouraging to those just starting to learn about the field -- be it students in this course, faculty interested in adding bioinformatics content to their courses, or the general Internet visitor. This page aims to organize, generalize and simplify by highlighting certain important bioinformatics resources.

Essential Information

This section contains links and information essential to the course content.

Review

• NCBI's Literature Database
• Molecular Biology Notebook
• Short (5 pages) Primer on Molecular Biology
• Molecular Biology & Genetics Primer for Mathematicians
• Dictionary of Genetic Terms

Part I: Sequence Databases and Information Retrieval

• NAR Molecular Biology Databases 2016 Update
  The journal Nucleic Acids Research publishes a yearly list of databases in the field. (See also Further Reading below)
• NAR Database Issue; NAR WebServer Issue
  The journal Nucleic Acids Research also publishes a yearly list of databases and web-servers for performing on-line tasks in bioinformatics and computational biology, all accompanied by excellent summary-guide papers.
• Entrez at the NCBI HomePage
  Entrez is the entry point for searching dozens of databases maintained by the National Center for Biotechnology Information (NCBI), including nucleotides (GenBank), proteins, genomes, 3D structures as well as literature and online full-text articles (PubMed).
• EMBL - Access EMBL through SRS or its EBI Services HomePag
  Maintained by the EBI, EMBL is the European member of the International Nucleotide Sequence Database Collaboration and contains DNA and RNA sequences.
• OBRC: Online Bioinformatics Resources Collection The Health Sciences Library of the University of Pittsburgh; a large collection of resources in a well-organized format.
• 2can Bioinformatics Tutorials - EBI offers instructions and tutorials on how to use its powerful computational tools and comprehensive databases.
• UniProt
  The world's most comprehensive catalog of information about proteins. Contains information from TrEMBL, SwissProt and PIR.

Part II: Pairwise Sequence Comparisons

Part III: BLAST, FASTA, and advanced BLAST

• BLAST
  Basic Local Alignment Search Tool from NCBI. Finds regions of local similarity between biological sequences (nucleotide or protein).
• FASTA
  FAST-All searching from EBI. Sequence similarity searching against nucleotide and protein databases.

Part IV: Protein Sequence and Structure Analyses

• Protein DataBank (PDB)
  PDB is the single worldwide repository for 3D structures of proteins.

Part V: MSAs or Multiple Sequence Alignments

• Clustal Omega
  ClustalW produces biologically meaningful multiple sequence alignments of divergent sequences.
• Phyre and 3D-PSSM
  Protein homology/analogy recognition

Part VI: Molecular Phylogenetic Analyses

• SCI-PHY (formerly Bête) - Subfamily Classification in PHYlogenomics
• MEGA 5.0 - Molecular Evolutionary Genetics Analysis; Ref#1; Ref#2
• BEAST (Bayesian Evolutionary Analysis Sampling Trees) for advanced users; Ref#1

For Further Reading

This section contains links to articles, websites and other resources for further reading on the topics covered in the course. All textbooks listed are on reserve at the Prevo Science Library unless otherwise noted.

The Textbooks used for this Course

• Bioinformatics and Functional Genomics by Jonathan Pevsner (2003), Wiley-Liss; Bioinfbook.org - Website dedicated to the text with updated URLs
• Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins; text web-site
• Understanding Bioinformatics

More Textbooks

• An Introduction to Bioinformatics Algorithms by N.C. Jones & P.A. Pevzner (2004), MIT Press
• Bioinformatics and Molecular Evolution by Paul G. Higgs and Teresa K. Attwood (2005), Blackwell Publishers
• Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, edited by Baxevanis & Oulette (2005), Wiley-Interscience
• Fundamental Concepts of Bioinformatics by D.E. Krane & M.L. Raymer (2003), Benjamin Cummings
• The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny edited by M. Salemi & A-M Vandamme, (2003) Cambridge University Press
• Statistical Methods in Molecular Evolution (Statistics for Biology and Health) edited by R. Nielsen (2005), Springer (not on reserve)
• Basic Mathematics for Biochemists (2nd ed.) by Athel Cornish-Bowden (2000), Oxford University Press (not on reserve)
• Beginning Perl for Bioinformatics by James Tisdall (2001), O'Reilly
• Mastering Perl for Bioinformatics by James Tisdall (2003), O'Reilly

Software and Other Programs

There are seven software programs listed in this section, and they are in a specific order -- one that echoes the flowchart of biological information used for this course.

• FinchTV - viewing DNA sequence traces
• SeWer (SEquence analysis using WEb Resources) - an integrated portal to common web-based services in bioinformatics
• Clustal Omega - multiple sequence alignment
• MEGA 7. - Molecular Evolutionary Genetics Analysis
  • Online Manu
• DAMBE (Data Analysis and Molecular Biology and Evolution)
• PAUP - tools for inferring and interpreting phylogenetic trees
• MrBayes - Bayesian inference of phylogeny

Review

• EBI Services - a collection of services offered by the European Bioinformatics Institute
• 2Can - bioinformatics tutorials from EBI
• NCBI - the homepage for the National Center for Biotechnology Information
• Bioinformatics and The Biology Student Workbench

Part I - Sequence Databases and Information Retrieval

• NAR Database Summary Pape - an alphabetical list
• NAR Research database issue 20
• Supplementary Table 1 [DOC] - a table of all databases listed in the NAR Molecular Biology Databases 2006 Update (or see alternate list at: UBiC)
• Gene Ontology - controlled vocabulary for describing gene and gene product attributes
• SMART - identification and annotation of protein domains

Part II: Pairwise Sequence Comparisons

• SMS - Sequence Manipulation Suite from Bioinformatics.org

Part V: MSAs or Multiple Sequence Alignments

• Hidden Markov Models (University of Leeds, UK)
• Wikipedia entry for hidden Markov models
• MAFFT - Fast Multiple Sequence Alignment
• MAFFT ver. 5
• MUSCLE - MUltiple Sequence Comparison by Log Expectation
• SATCHMO - Simultaneous Alignment and Tree Construction using Hidden Markov mOdels
• FlowerPower - clustering of homologous proteins

Other Links

This section contains links to various online resources that are not directly connected to course material, but students, faculty and other parties interested in bioinformatics may find useful.

Genome and Genomics

• Human Genome Project Science
• Dictionary of Genetic Terms - from Genomics 101: A Primer
• Project Ensembl
• TIGR - The Institute for Genomic Research

Education

• GeoSpiza's Bioinformatics in Education
• ISCB Listing of Degree/Certificate Programs Worldwide
• Human Genome Project Science
• Bioinformatics Data Mining Exercises
• Genome Consortium for Active Teaching (GCAT)

Model Organisms

• MGI - Mouse Genome Informatics
• Zebrafish Genome
• Wormbase - (c.elegans)
• BDGP - Berkeley Drosophila Genome Project
• FlyBase - A Database of the Drosophila Genome
• TIGR-CMR - Comprehensive Microbial Resource
• Saccharomyces Genome Database

Last updated: April 3rd, 2017; Andrew Klein and Chet Fornari