Genome Analysis

• Complete Microbial Genomes @INFOBIOGEN

• Uncomplete Microbial Genomes @INFOBIOGEN

• Blast with Microbial Genomes @NCBI

• SALSA DNA and Protein Sequence Database Search against complete genomes @Norway

• COG Clusters of Orthologous Groups @NCBI

• ORF Finder @NCBI

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Multi-Service Servers

• NCBI @National Center for Biotechnology Information

• EBI @European Bioinformatics Institute

• BCM Search Launcher @Human Genome Center, Baylor College of Medicine, Houston TX

• embNet.org-Part of the Swiss Institute of Bioinformatics

• GenomeNet @Kyoto University, Japan

• PÙle Bio-Informatique Lyonnais @France

• The Biology WorkBench @SDSC

• IDEAS Integrated Database and Extended Analysis System for Nucleic Acids and Proteins (@Japan)

• Sequence Analysis on the Web @Jena

• Webgene server @Italy

• ANTHEPROT (ANalyse THE PROTeins)

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Homology Search Engines

• BLAST search page @NCBI

• BLAST search page @GenomeNet, Kyoto, Japan

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Alignments

• BOXSHADE 3.21 Pretty Printing and Shading of Multiple-Alignment files

• CLUSTALW @PBIL, France

• Multiple Protein Sequence Analysis @PBIL, France

• Consensus @the Bork group, EMBL

• Tools for Alignment at the Bork group

• Divide-and-Conquer Multiple Sequence Alignment for high quality simultaneous multiple sequence alignments

• DIALIGN 2 especially suited to detect local similarities among distantly related sequences

• Multiple Alignment

• Multiple Alignment Resource Page

• TMAP

• ALIGN Compendium of Protein Sequence Alignments

• SeaView

• CINEMA Colour INteractive Editor for Multiple Alignments

• LalnView @PBIL

• Match-Box Web Server 1.2 multiple sequences alignment of proteins @Belgium

• VSNS BioComputing Division Multiple Alignment Resource Page

• Alignment Search software @EBI

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Motifs and Searches

• MOTIF Searching Protein Sequence Motifs

• PRINTS Protein Motif Fingerprint Database

• Protein Functional Analysis at BMERC

• ScanProsite Protein against PROSITE

• THE MEME/MAST SYSTEM

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Domains

• PFAM @WashU.

• ProDom protein domain database

• Multicoil predicts the location of coiled-coil regions

• Paircoils predict the location of coiled-coil regions

• PROSITE Dictionary of protein sites and patterns

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Phylogenetic Analysis

• Introduction to Phylogeny

• Phylogeny and Evolution @Univ of Oxford, UK

• Taxonomy and Systematics @Univ of Glasgow (software)

• NJplot for parsimony, distance or maximum likelihood trees

• Unrooted

• Phylo_win for neighbor-joining, parsimony and maximum likelihood methods

• PHYLIP a package of programs for inferring phylogenies

• Molphy phylogenetic analysis with (ML) and (NJ)

• PUZZLE Tree reconstruction for sequences by quartet puzzling and maximum likelihood

• Phylogenetic Tree prediction Putative phylogenetic trees prediction for sequence multiple alignment by cluster and topological algorithms

• TreeView

• MacClade

• Phylogeny and Reconstructing Phylogenetic Trees

• Phylogenetics Software Resources

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Structure

• PDB

• The Dali server comparing protein structures in 3D @EBI

• NDB Biological Structure Resource @Rutgers Univ

• SCOP Structural Classification of Proteins

• FSSP - Fold classification based on Structure-Structure alignment of Proteins

• The PredictProtein server (@EMBL)

• RasMol Home Page to display molecular structure

• PHD Predict Protein Secondary Structure @EMBL-Heidelberg

• Antibody Structure and Sequence Information

• NNPREDICT Protein Secondary Structure Prediction

• PREDATOR Protein secondary structure prediction from single sequence or a set of sequences (@EMBL)

• Protein Motions Database

• Image Library of Biological Macromolecules @JENA

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Transcription

• WWW Signal Scan

• WWW Promoter Scan

• DPInteract: DNA-Proteins interactions db

• AG BIODV @Neuherberg, Germany

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Sequence Reference and Retrieval-System

• Entrez The NCBI WWW Entrez Browser

• Sequence Retrieval System- SRS Network Browser for Databanks in Molecular Biology (@EBI)

• ExPASy top page

• PROSITE Dictionary of protein sites and patterns

• Query Databases @EBI

• GeneCards human genes, proteins and diseases @Weizmann Institute

• SEQNET access to all major molecular biology sequence and structure databases and programs

• DBGET Integrated Database Retrieval System @GenomeNet, Japan

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Gene

• GeneMark @EBI

• PROCRUSTES gene recognition algorithm @Los Angeles, USA

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DNA

• Correspondence Analysis of Codon Usage @Oxford, UK

• RepeatMasker screens DNA against a library of repetitive elements and returns a masked query sequence ready for database searches

• Oligo Calculator Tm, Mw, OD, GC% @UPENN

• Tm Determination

• dbEST Database of Expressed Sequence Tags at NCBI

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RNA

• ESSA an integrated and interactive computer tool for analyzing RNA secondary structure @France

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General

• PSORT Prediction of Protein Sorting Signals and Localization Sites in AminoAcid Sequences

• GPCR Pattern Recognition

• PROCRUSTES Gene Recognition via Spliced Alignment

• Buffer calculator

• Sequin for submitting entries to the GenBank, EMBL, or DDBJ sequence databases

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Links

• Pole Bio-Informatique Lyonnais @France

• Sequence comparison

• The BioCatalog a software directory @EBI

• Pedro's BioMolecular Research Tools

• Pedro's BioMolecular Research Tools Molecular Biology Search and Analysis

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