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Bioinformatics Tools and Software

Database Searching 

Entrez (NCBI)
Query GenBank database (NCBI)
Sequence retrieval system (SRS, EBI)
PDB search
Swissprot (ExPaSy)|
BLAST (NCBI)
Fasta (EBI)
The PredictProtein server

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Motif Identification

InterPro (EBI)
Prosite (ExPaSy)
Pfam (The Sanger Centre)
Prodom (INRA, Toulouse)
SMART (EMBL)
PRINTS (University of Manchester)
Hidden Markov Models: theory
HMMER 2.1.1: to build up HMMs
Hidden Markov Models: links

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Multiple Sequence Alignments

Clustalw at EBI
Clustalw at Pasteur
MultAlin
Match-Box
Dialign2 (2 sequences)
Blast2 (2 sequences)
Jalview

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Protein Analysis

Compute pI/Mw 
ORF finder at NCBI
TranslatER: Translate a DNA sequence
SAPS: Statistical Analysis of Protein Sequences
ProtScale: hydrophilicity/hydrophobicity 

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Protein Pathway Analysis

DIP: Database of Protein Interactions
KEGG: Kyoto encyclopedia of genes and genomes
MIPS: yeast pathways
Transpath: signal transduction database
CSNDB: Cell signaling

Protein Secondary Structure

PDB (Protein Data Bank)
CATH (UCL)
SCOP (MRC-LMB)
FSSP (EBI)
AGADIR (EMBL)
HNN (Pole Bio-Informatique Lyonnais)
SwissModel (ExPaSy)
CPH (Technical University of Denmark)

Genome Sequencing

TIGR: The Institute for Genomic Research
Proteome Inc. (YPD, WormPD)
MIPS: Munich Information Center for Protein Sequences
Stanford genomic resources (SGD,ATdb)
GOLD v.1.0: Genomes On Line Database
Genome analysis (MRC LMB)

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Repetitive DNA

Satellites: Identifies satellites and periodic repetitions
Repeats: Microsatellite-type regions

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Analysis of regulatory regions

MatInspector: binding site prediction  
Promoter Scan:promoter prediction
Signal Scan
TFBIND
PROMO
The Promoter Database of 
Saccharomyces cerevisiae
Pratt: Find patterns   
Jaak Vilo homepage:expression, clustering, patterns
TRANSFAC: Transcription Factor Database
EiPD: Eukaryotic Promoter Database  
Genome-Wide Expression:Young's lab
TRRD:Transcription Regulatory Regions Database, Nobosibirsk
GeneExpress system,Nobosibirsk
TRADAT: TRAnscription Database and Analysis Tools
Muscle-Specific Regulation of Transcription

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Statistics

Statistics programs
The Statistics of Sequence Similarity Scores

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Programming Resources

CPAN Perl
Bioperl