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DNA/RNA Tools

• Bacteria Transformation Efficiency Calculator

• BCM Search Launcher: Sequence Utilities

• Biology, Biotech Companies Directory

• Cis-elements Nucleotide Count Matrices

• CISTER Cis-element Cluster Finder

• Cluster Buster

• Codon Usage

• Color Align Conservation

• Combine Fasta

• CpG Islands

• DNA Molecular Weight Calculator

• DNA Pattern Finder

• DNA to Protein Translation

• EMBL Feature Extractor

• EMBL to FASTA

• EMBL Trans Extractor

• Fuzzy Search DNA

• Fuzzy Search Protein

• g force rpm calculator

• GC Skew Tool

• GenBank Feature Extractor

• GenBank to FASTA

• GenBank Trans Extractor

• GENSCAN at MIT (US)

• GEO Gene Expression Omnibus

• Grand average of proetin hydropathy Calculator

• Graphical Codon Usage Analyser

• Identity and Similarity of Sequences

• JustBio Sequence Cleaner

• JustBio Translator

• McPromoter promoter prediction

• MEME - Motif based sequence analysis

• Motif search -- Improbizer

• Multi Reverse Translation

• Multiple Sequence Alignments

• NetPrimer (US)

• New England Biolabs Enzyme Finder

• OD260 Nucleic Acid Concentration Calculator

• Pairwise Align Codons

• Pairwise Align DNA

• PCR Box Titration Calculator v 0.93

• PCR Primer Map

• PCR Primer Stats

• PCR Product Size Calculator

• Phylip online

• POSSUM detects cis-elements

• Random sequences

• Ranodm Coding DNA

• Reading Sequence Aloud

• Restrict Digest

• RNA folding (Zuker; mirror in Australia)

• Secret Coder Tool

• Sequence Massager

• Six Frames Translation

• Skew plots (MIPS Munich)

• SSR Simple Sequence Repeats Extractor

• Standard Deviation Calculator

• TFSEARCH Transcription Factor Binding Sites

• The Sequence Manipulation Suite

• TRF Tandem Repeats Finder

• Web Primer_ DNA and Purpose Entry

• WebGeneMark

• WWW GeneFisher (Germany)

• Zlab Gene Regulation Tools

Protein Sequence Analysis

• 2ZIP Leucine zipper prediction

• 3D-PSSM Protein Fold Recognition

• amino acid structures

• Antigenicity Plot

• CE -- 3Dcomparison & alignment

• CODEHOP (based onprotein alignment)

• CPHmodels - Homology modelling

• DNA Size (kb) Protein Size (kDa) Conversion

• drawhca -- Hydrophobic Cluster Analysis plot

• Entrez Structure at NCBI

• ExPASy - SWISS-3DIMAGE

• Filter Protein

• GENO3D -- Protein 3D Structure

• Group Protein

• Hydropathicity Plots

• InterProScan

• Modified and unusual amino acids

• Molecules-R-US

• Motif Scan (ISREC)

• MOTIF Searching Protein and DNA

• OPO2 Transmembrane Protein Display

• Physical-chemical AA classification

• PRATT (EBI)

• PredictProtein - Structure Prediction

• Primer predict of protein alignment

• Proetin Pairwise Alignment Tool

• PROSITE at EBI (Hinxton, UK)

• PROSITE at ExPASy (Switzerland)

• PROTCOMP -- sub-cellular localization

• Protein Isoelectric Point Calculator

• Protein Molecular Weight Calculator

• Protein Pattern Finder

• Protein Stats

• Protein Structure Prediction (HMM based)

• Protein to DNA Translation

• PROWL

• PROWL - Amino Acid Properties

• PSIPRED protein structure prediction

• PSORT -- predict protein localization

• Radar Repeats in proteins

• RandSeq -- Random protein sequence generate

• Ranodm Protein Sequence

• REPv1.1 Repeats in proteins

• Reverse Translation (all possibilities)

• Reverse Translationbased oncodon usage)

• SMART - Simple Modular Architecture

• TargetP-- predict subcellular location

• TMHMM - transmembrane helices predict

• TMpred -- Transmemebrane prediction

Sequence Similarity/Alignment and Phylogenetics

• AA composition protein search (ExPASY)

• Alignment (MichiganTech, US)

• BCMPairwise Sequence Alignment

• BLAST (Japan)

• BLAST (NCBI)

• BLAST at EBI (UK)

• BLAST2SRS retrieval tool - protein only (EMBL)

• BoxShade Server (Switzerland)

• CINEMA (Color Editor for Alignments)

• CLUSTALW at BCM (USA)

• CLUSTALW at EBI (UK)

• Dali -- protein3-Dstructure compare

• DIALIGN (BiBiServ)

• Do-It-Yourself WU-Blast

• DOT PLOT (Colorado State University)

• DOT PLOT FLAG (Taiwan)

• DOTMATCHER (Emboss)

• FASTA at EBI (UK)

• LALIGN (local) at MBDC (Oxford, UK)

• LALIGN (local) at University of Virginia (USA)

• MBS - ALIGNER

• MPsrch Smith Waterman at EBI (UK)

• MUSCLE protein sequence alignment

• OWL BLAST Server

• PFAM

• PipeAlign DbClustal

• PROPSEARCH at InfoBioSud

• Rose random model of sequence evolution

• SAM_ Sequence Alignment and Modeling

• SplitsTree (BiBiserv)

• T-COFFEE server

Databases and Resources

• AcroMed -- a database of biomedical acronyms

• Amino Acid and Codon Table

• Amino Acid Properties

• ARGH -- Biomedical Acronym Resolver

• BCCM

• BMERC Completed Genomes collected

• BWS -- BIOSMILE web search

• Codon Usage Database

• COG Clusters of Orthologous Groups

• COPE -- Cytokines Online Pathfinder Encyclopaedia

• DBTss

• dcode

• DNA Structures

• EPD(promoter)

• ERGO (Integrated Genomics, Inc.)

• Genome Channel (Oak Ridge, US)

• Genome Monitoring Table (daily update EBI)

• GOLD Genomes Database

• HOBACGEN Homologous Bacterial Genes Database

• Huge Index Database

• Jaspar(TF binding DB)

• KEGG

• LSPD

• NCBI Complete Microbial Genomes

• NCGR National Center for Genome Resources

• Organism-specific Databases

• PEDANT CrossGenome categories

• PEDANT front page

• Protocol On-line

• PubMed Home

• Restrict Enzyme Domain

• SPD

• Tavi's PCR protocols

• TaxPlot (NCBI)

• TIGR

• Tiprod(promoter)

• WIT Home Page

Genome Projects

• 1000 Genomes Project

• Arabidopsis thaliana

• Berkeley Drosophila Genome Project

• C. elegans project

• Cancer Genome Project

• DDBJ Genome Information Broker

• DNA Structural Analysis Sequenced Genomes

• Elephant Shark Genome Project

• Genome Projects Database (NCBI)

• GOLD Genomes OnLine Database

• HapMap Project

• Horse Genome Project

• Ixodes Genome Project

• Leishmania Genome Network

• Malaria Genetics & Genomics

• PEDANT complete genomes

• Personal Genome Project - Public Profile

• Retroviruses

• Rice Genome Annotation Project

• Structural Analysis of Microbial Genomes

• The Maize Genome Browser

• The US Poultry Genome Project Website

• TIGR Microbial Database

• Trypanosoma brucei Genome Project

Free Biology Software

• ANTHEPROT -- Protein 3D

• Artemis -- Sequence annotation and Viewer

• Asterias -- genomic data analysis

• BioEdit -- Sequence Alignment Editor

• BioRainbow -- Binding Site Prediction

• CHROMAS -- Chromatgram file viewer

• Clann -- Phylogenetics

• CLC free workbench

• ClustalX -- Sequence alignment

• CURVES -- Helical Analysis

• Dnasp -- DNA Plymorphism

• GoCore -- Protein Analysis Excel Add-in

• ISYS -- Biotools integration

• JaDis -- Ka Ks Calculation

• LDhat -- Recombination Analysis

• Mega -- Phylogenetic

• pDRAW32 -- Plasmid Map Draw

• Phylogeny software Series

• RasMol -- Molecule 3D viewer

• RDP -- Recombination Detection

• SeaView -- Phylogenetic

• Sequin -- NCBI Submission_

• SeqVerter -- Sequence format converter

• Visual Cloning -- DrawPlasmid Map

Miscellanous

• Biocompare -- the Buyers' Guide

• Faculty of 1000

• Free Patent Online

• Google Scholar

• HSLS

• Journal Impact Factor

• Open Access Journals

• Protocol On Line

• ScienceDaily Biology

• Scopus - reference citation database

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