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• Human Genome Project Information

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Microarray Data Analysis

Microarray software Suite TM4 includes the following (free for download) packages:

• 1. MADAM: MicroArray DAta Manager - Facilitates the entry of microarray data into a relational database.

  2. Spotfinder - Analysis of microarray images.

  3. MIDAS: Microarray Data Analysis System - Normalization and filtering of microarray data.

  4. MeV -Multi-Experiment-Viewer - Includes several methods for analysis of microarray data.

Database Searching

BLAST Server - Sequence searches at NCBI.

Bioccelerator - Sequence searches at EMBL.

Database searches - EBI.

Database searches at DISC (Japan) - Includes Fasta, BLAST, MPsrch and SRS Fasta.

Match sequence against PROSITE

Multiple Sequence Alignment

PRALINE - Multiple sequence alignment.

T COFFEE - Multiple sequence alignment.

Clustal W - Multiple sequence alignment.

SAM - Sequence alignment and modeling system (using HMMs).

AMAS - Analysis of multiple alignments (Geoff Barton).

HMMER - Multiple sequence alignment.

DIALIGN 2 - Multiple sequence alignment.

Secondary Structure Prediction

PredictProtein - Server to predict protein structure.

PSI-Pred - PSI-BLAST-based protein secondary structure prediction.

YASPIN - Server to predict protein secondary structure.

Modelling and Data analysis

DALI - Comparison of protein structures in 3D.

Pratt - Pattern discovery online.

Expression Profiler - Online tool for expression profile clustering and sequence pattern discovery.

PSA - Protein Sequence Analysis: fits a structure model to your sequence.

Block Maker - Fred Hutchinson Cancer Research Center.

MEME - Multiple EM for Motif Elicitation.