Bioinformatics Tools
BLAST
ExPASy: Comprehensive bioinformatics resource portal 
SoftBerry: Comprehensive bioinformatics resource portal
RAST: The NMPDR, SEED-based, prokaryotic genome annotation service
Secondary Metabolites Bioinformatics Portal: More tools and databases

SBSPKSv2:  Prediction of PKS products and rational design of engineered polyketides  
PKS-NRPS Analysis: in silico pathways prediction method by Bachmann et al. 
antiSMASH: A program for antibiotics & secondary metabolite prediction from genes
BAGEL4: automated bacteriocin mining

Clustal Omega: multiple sequence alignment program for DNA or proteins
ESPript: drawing tool for multiple sequences aligment 
FramePlot: ORF prediction for high GC-content bacteria 
HHpred: Homology detection & structural prediction by HMM-HMM comparison 
CODEHOP: Consensus-degenerate hybrid oligonucleotide primers design
SignalP: A program for signal peptide cleavage sites prediction from protein sequences
LipoP: Prediction of lipoproteins and signal peptide cleavage sites from protein sequences
ProtParam: Computation of various physical and chemical parameters for proteins
TOPCONS: Membrane protein topology prediction
Protter: Protein sequence and topology visualization
XtalPred-RF: Prediction of protein crystallizability

Genomes & Enzymes Databases
BRENDA: A comprehensive enzyme information system 
E. Coli Genotypes
SMURF: Secondary metabolites biosynthetic gene discovery in fungal genomes
JGI Genome Portal: Comprehensive microbial genomes collections
Pseudomonas aeruginosa Transposon Insertion Mutant Library
Pseudomonas Genome Database
REBASE: NEB-curated database of putative restriction-modification systems
ThYme: Thioester-active enzymes database

Other Useful Tools & Information
Ammonium Sulfate Calculator: For estimating protein precipitation conditions
XCMS: Metabolomics analysis
PRIMe RIKEN: Metabolomics software and mass spectrum prediction (MS-FINDER)
Molecular Formula Search: HRMS weight to molecular formula program
Mass Spectrometry Adduct Calculator
Fatty Acids: an integrated website for fatty acids properties
NEB Tm Calculator
Molarity Calculator
Reaxys: Chemistry search engine
Dictionary of Natural Products