bioinformatics

Matouschek Lab

Department of Molecular Biosciences Northwestern University

Northwestern University | Northwestern Search

Center for Cell and Developmental Systems Biology | Department of Molecular Biosciences

2205 Tech Drive, Hogan 2-100, Evanston, IL 60208

Lab phone: (847) 467-3530 Lab fax: (847) 467-6489 Email the Webmaster

Primary Structure Analysis

ProtPram : Calculate physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.) (ExPASy)

The Sequence Manipulation Suite: A collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences

Sequence Similarity

Pairwise BLAST : (Similarity Search between Two Sequences)

BLAST : Sequence Database Search Tool (NCBI)

FASTA : Protein Sequence Database Search Tool (NPSA)

Multiple Sequence Alignment

Clustal W : at European Bioinformatics Institute, EMBL

Clustal W - Proteins : at Network Protein Sequence Analysis

Clustal W - DNA : at NPSA

Phylogenetic Tree Construction

Phylip programs

Structural Alignment

DALI : Structural Similarity Tool

FSSP : Fold classification based on Structure alignment of Proteins

Secondary Structure Prediction

PredictProtein - Secondary Structure Prediction Tool

PHD : PHD Secondary Structure Prediction Method at NPSA

SOPMA : SOPMA Secondary Structure Prediction at NPSA

Advanced Primary Structure Analysis

ExPASy : Proteomics Tools

EMBL-European Bioinformatics Institute

Pfam : Protein families database of Alignments and HMMs (Sanger)

PatScan : Scan Sequence Database for Patterns

PattinProt : Pattern Search at NPSA

Profile Scan : Motif Search in a Protein Sequence

Scan Prosite : Search Protein Sequence for Profiles at Prosite

SMART : Simple Modular Architechture Research Tool at EMBL

Homology Modeling

Swiss-Model : Homology Modeling Tool