Computational Biology Tools & Databases

• RNA Secondary Structure Related
  • Vienna Package
  • SRPDB
  • tmRNA
  • Ribosomal Database Project II
  • PseudoBase
  • Gutell Lab Comparative RNA Web
  • RNA links
  • tRNA sequences compiliation
  • Jenna RNA world
  • ILM by me for RNA pseudoknots
• Rice Genome Related
  • Rice Genome Research Project
  • National Center for Gene Research Chinese Academy of Sciences
  • TIGR Rice Genome
  • Rice unigene
  • RGP Link Page
• Promoter/TF Databases
  • PlantProm - A database for Plant Promoters
  • EPD - Eukaryotic Promoter Database
  • PLACE - A Database of Plant Cis-acting Regulatory DNA Elements
  • TRANSFAC - The Transcription Factor Database
  • TRRD - transcription regulatory region database
  • ooTFD - Object-oriented Transcription Factors Database
  • COMPEL - Database on composite regulatory elements
  • PlantCARE - a databse of plant promoters and their cis-acting elements
    
  • SCPD: The Promoter Database of Saccharomyces cerevisiae
• General Tools and Database
  • WU-BLAST2
  • ClustalW
  • SRS @ the EBI
  • Phylogenetic analysis
  • RSA tool

Machine Learning and Data Mining

• Weka 3: Machine Learning Software in Java
• weka API

Conferences

• RECOMB
• RECOMB Satellite Conferences on Systems Biology
• ISMB
• ECCB
• PSB previous proceedings
• CSB
• ICSB
• AAAI
• ICDM
• KDD
• ICML

Journal Collections

• UTSA library
• CiteSeer
• DBLP
• ScienceDirect
• Journal Storage
• PubMed
• ACM digital library
• BioMedNet
• BioMed Central
• Bioinformatics and Systems Biology Electronic Library

• Science
• Nature
• Bioinformatics
• Journal of Computational Biology
• Nucleic Acids Research

• Individual author's publication pages
• Journal Impactor Factors

• My literature compilations
  
  • ABA genes and motifs
  • Motif finding

Programming

• C/C++
  • Programming in C
  • C Programming
  • Dinkum C++ library
  • the C++ Annotations
• Java
  • Biojava.org
  • Sun's Java page
  • Sun's Java Tutorial page
  • Java1.5 API spec
  • Apache Ant 1.5 Manual
• Perl
• Learning Perl
• Perl Manual at CMU
• Perl Tutorial at UIUC
• Shell Script
  • linux shell Scripting tutorial (Bash)
  • Bourne Shell Programming Tutorial
  • Advanced Bash-Scripting Guide
  • The C Shell
  • C-shell Cookbook
• Algorithms
  • Data Structures and Algorithms with Object-Oriented Design Patterns in C++
  • Data Structures and Algorithms with Object-Oriented Design Patterns in Java
  • The Stony Brook Algorithm Repository

Linux Misc

• Linux Documentation Project Guide
• Linux tutorial
• Mastering the VI editor
• Vi Tutorial
• Make - a tutorial
• sed tutorial
• a collection of tutorials (shell, admin, c/c++, vi, etc.)