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  Initial Bioinformatic Investigation
Using Bioinformatic Tools to Strategically Design Expression/Purification Projects

Dr. Nurit Kleinberger-Doron
The various bioinformatic tools are sorted by:
Rationale Project Design
Additional Tools

Your comments are most welcome.

Entries since November 2003

Bioinformatics Tools Sorted according to Rationale Project Design

Preliminary Search of Databases Before Starting a Project
Using Keywords

Most recommended: NCBI, EBI, Genecards, Brenda 
Additional options: Nucleic Acid Research List

Using Sequence

Sequence alignments (pairwise & multiple alignment)

Sequence Analysis Using Software & Databases
DNA/RNA Sequences

A. Secondary structure of mRNA
B. Problems due to differences in genetic code
    1. Rare codons, 2. Different genetic codes) 
C. Alternative splicing
D. Ribosome binding site

Protein Sequences
A. Motifs and Repeats in  Proteins
B. Physicochemical properties
C. Experimentally determined protein structures
D. Structure and function predictions
E. Subcellular localization & signal peptides
F. Co- and Post-translational Modifications (including S-S bonds)
G. Protein degradation
    1. Protein turnover 2. Proteolytic cleavage
H. 1. Protein-protein interactions  2. Biological Pathways
I. Additional Tools


Bioinformatics Tools Sorted by Expression Problems

Possible Causes
Bioinformatics Tools
Very low amounts of expressed proteins
  • Secondary structure of mRNA 
  • Rare codons 
  • Low t1/2, 
  • Secretion signal
Truncated forms
  • Rare codons 
  • Genetic code differences [trp-stop] 
  • Additional RBS [consider GUG too] {alternative reading frame}
  •  Proteases during induction or lysis
  • Cloning out of frame
Insoluble protein
  • Post-translational modifications
  • S-S bonds 
  • Partners in complex 
  • Localization signals 
  • Transmembrane domains 
  • In-frame mutation/s due to rare codons or non-standard genetic code

Additional Tools & Databases


Preliminary Search of DatabasesBefore Starting a Project

Preliminary Search Using Keywords

Sequence-based Preliminary Search & Sequence Alignments
DNA & RNA Sequence Analysis

Secondary Structure of mRNA

Codon Usage and Translation Frames

Alternative Splicing

Ribosome Binding Site (Background)

Protein Sequence Analysis

Motifs and Repeats in  Proteins

Physicochemical properties

Protein Turnover

Proteolytic Cleavage

Co- and Post-translational Modifications (A short summary)


Sub-cellular Localization and Signal Peptides

Subcellular Compartments

Targetting Peptides

Protein-Protein Interactions

Biological Pathways Experimentally Determined Protein Structures

Search for known structures using:

Structure Classification

Structure & Function Predictions

Secondary Structure Prediction
Domain Prediction
Topology Prediction
a helices    b sheets
Helical Wheels
Function Prediction

Function Prediction

Secondary Structure Prediction

Disordered Proteins

Domain & domain-linker Prediction 

Topology Prediction

a helices

b sheets Helical Wheels Additional Tools

This site is maintained by Dr. Nurit Doron . Your comments are most welcome.

entries since November 2003

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