Useful Scientific resources
Bioinformatics software/database
1. antiSMASH: antibiotics & secondary metabolite analysis shell.
2. RODEO: algorithm for the analysis of biosynthetic gene clusters, with an emphasis on RiPPs .
3. BLAST: finds regions of similarity between biological sequences.
4. Consurf: identifies conserved residues in homologous proteins.
5. EFI-Enzyme Similarity Tool: tool for generation of sequence similarity networks.
6. HHPred: secondary structure homology prediction.
7. Integrated Microbial Genomics (IMG): analysis, annotation, and distrubtion of microbial genome datasets.
8. InterPro: functional analysis of proteins by classification into familes, predicting domains and important sites.
9. UniProt: a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
10. Clustal Omega: multiple sequence alignment program.
11. MUSCLE: multiple sequence alignment creation.
12. PRISM: bioinformatic tool for the identification of unknown, genetically encoded natural products found within an input sequence.
13. PyMOL: 3D Molecular Visualization.
14. Protein Data Bank: repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids.
15. Skylign: logo creation.
16. NEB Tools and Resources: interactive tools from NEB for research and experimental design.
17. Expasy-Translate: translation of a nucleotide sequence to a protein sequence.
18. Expasy-ProtParam: computation of various physical and chemical parameters for a given protein.
19. PeptideCutter - Expasy: predicts potential cleavage sites cleaved by proteases or chemicals in a given protein sequence.
20. PeptideMass - Expasy: computes the masses of the generated peptides.
21. IDT OligoAnalyzer: calculates properties of oligonucleotides.
22. RadicalSAM.org: RadicalSAM.org enables the use of the EFI's genomic enzymology web tools for studies of the radical SAM superfamily.
23. MIBiG: database of biosynthetic gene clusters.
24. KEGG: Kyoto Encyclopedia of Genes and Genomes: database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
25. BRENDA : The Comprehensive Enzyme Information System.
26. STRING: database of known and predicted protein interactions.
Microbiology Culture Collection
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