BIO-SUITE
Protein and DNA interrogation site
........reliable bioinformatics tools
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Sequence Massager
Protein sequence
Protein 2D and 3D structure
Subcellular Location
BACKTRANSLATE
RADAR - repeat regions
Protein hydrophobicity
Amino acid composition
Protein Repeats
PROTPARAM amino acid %
Compute pI and MW
Physico-chemical colouration
PEPTIDE BUILDER
NNPredict - simple secondary structure
PSI-PREDICT - secondary and transmembrane topology
TOPPRED - Hydrophobicity Plot
PROTSCALE - Secondary structure
JPRED - secondary structure
GLOBPLOT - Protein disorder
TMPRED - transmembrane prediction
TMHMM - inside/outside predictions
PHYRE - 3D structure Preciction
GOR IV - secondary structure
PLOC
SUBLOC
ESLPRED
BaCello
WOLF PSORT
Nuclear Localization Sequence
Peroxisomal Targeting Signal PTS
PREDOTAR plastids and mitochondria
CELLO - comprehensive localisation tool
NUC-PLOC - subnuclear localisation
Nuclear sub-compartment prediction
MITOPROT - mitochondrial prediction
PSORTb - bacteria
PSORT II
SHERLOC
PROTCOMP
MULTI-LOC
SLP-LOCAL
TargetP
Searches & Alignments
Sequence Editing
BLAST
Advanced BLAST
ImageJ- Analysis of Gels and Micrographs
DbClustal - align BLAST searches
Colour DNA or protein sequences
CLUSTALW - align multiple sequences
DNA manipulator - reverse complement
Consensus Maker
Secret DNA decoder!
LALIGN
DALIGN
Sequence Massager -excellent manipulator
BOXSHADE - customise your alignments
Blast2seq - BLAST 2 sequences
Transcription/Translation Tool
PROTPARS - protein phylogenetic tree
Protein domain creator
PFAM - protein families
PrettySeq - DNA editor
Protein Duster
DNA Sequence Tools
ARTEMIS - genome viewer/manipulator
NEBCUTTER2 - Restriction analysis
REBSite -in silico gel digestion
SiteFind - Introduce a silent mutation
WATCUT - restriction analysis
PlasMapper - auto-annotate plasmids
Translate both DNA strands to protein - graphical output
Translate DNA in all frames
Translate with alignment output
CODON USAGE
CLONE-IT - subcloning strategy designer
Pathogen resources
Bacterial genomes - EBI
BACTERIAL VIRULENCE FACTORS
NMPDR - National Microbial Pathogen Data Resource
Virulence Database
Bacterial Genomes - Sanger Centre
ModLab -Effector protein predictor
‘Effective’ - Effector predictor
PCR & Primer Software
PrimerX - make mutagenic primers
Primer3 - pick best primer sets
OligoPerfect - primer designer
Primer analyzer - Tm, hairpins, primer-dimer
iPCR - test your primers in silico
GENEFISHER - excellent primer designer
Free Microscopy software
Leica LAS AF Lite - Free Confocal software (for .lif files)
Zeiss LSM Image viewer
Aziovision Lite - view .zvi files
VOLOCITY LE - free but requires registration
Bacterial Gene and Promoter Prediction
Promoter Predictor - Pro/Eukaryotic
BPROM -find promoters
ORFinder - excellent tool from NCBI
GLIMMER - NCBI gene finder
GENEMARK - another NCBIgene finder tool
Bio-calculating
Molarity calculator
% nucleoltide composition
GEECEE - % GC
Convert centrifugal RPM to RCF (g)
Buffer design and calculation
Databases and Software Collections
EXPASY.ORG - protei software
SOFTBERRY bioinfomatics suite
Sequence Mainpulation Suite
KEGG - genes and genomes
Sanger Centre - genomes
NCBI - genomes and software
TIGR - genome databases
EMBL-EBI databases and software
INTEGR8 -proteomes & genomes
PBIL.ibcp.fr
ProteinMotifs Discovery
BLOCKS search protein against BLOCK database
NCBI - conserved domains
ELM server - eukaryotic motifs
NetPhos 2.0 phosphorylation sites
GPI Predictor
ProScan - Protein domain discovery
SMART - Protein modular architecture
PROSCAN - protein motifs
KEGG MOTIF
MOTIF SCAN
PRINTS - search the FPRINT database
Lab aids - Plasmid PDF
Cloning Aids
Bacterial
pET-28a
pACYC184
ptrc99a
pBluescript SK
pBR322
pUC19
Mammalian
pDsRed1-N1
pECFP-C1
pEGFP
pEGFP-C1
pEGFP-C2
pEGFP-N1
pEGFP-N3
Restriction digests close to the end of DNA (NEB)
Genetic Code
Qiagen’s Molecular Biology Bench Guide
Qiagen’s quantitation of DNA
Microbiology and Pathogen Journals - the Hot List
pIRES-EGFP
