Useful Online Tools

Note: The descriptions of the tools listed below have been taken from the respective websites.

NEBcutter V2.0: This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence. 

ExPASy: ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. 

BLAST: Basic Local Alignment Search Tool, BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. 

PUBMED: PubMed comprises more than 28 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. 

Net Primer: Free! Primer Analysis Software. User account creation required.

GenomeNet: GenomeNet is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences, operated by the Kyoto University Bioinformatics Center.

ROBETTA: Full chain protein structure prediction software

Carl Zeiss Microscopy Online Campus: The Carl Zeiss Microscopy Online Campus website explores the fascinating world of optical microscopy and provides the necessary background to understand both the basic concepts and advanced principles.

Olympus Microscopy Resource Center

Addgene: Non-profit plasmid repository

DeepView - Swiss-PdbViewer: Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

NetNGlyc 1.0 Server: The NetNglyc server predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. 

NetOGlyc 4.0 Server: The NetOglyc server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. 

SignalP 4.1 Server: SignalP 4.1 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. 

K2D2: Estimating protein secondary structure from CD spectra

K2D3: Estimates protein secondary structure from CD spectra

Bestsel: BeStSel (Beta Structure Selection) is a novel method for the secondary structure determination and fold recognition from protein circular dichroism spectra.

Oligo Calculator: Calculate melting temperature of oligo

GenScript Rare Codon Analysis Tool: Rare Codon Analysis Tool is powerful for codon usage frequency of your sequence and codon usage distribution. It can help you decide if your sequence needs to be optimized for heterologous gene expression.

Weight to Molar Quantity (for proteins): This is used to convert the weight (weight concentration) into the molar quantity (molar concentration) for proteins, and vice versa.

ResFinder 3.0: Identifies acquired antimicrobial resistance genes and/or find chromosomal mutations in total or partial sequenced isolates of bacteria.

Bacterial Bioinformatics Resource Centre: Genome integrated Data and Analysis Tools; Genome Assembly, Genome Metadata, Genome Annotation

MLST 1.8: Multilocus Sequence Typing Data for Global Epidemiology of Pathogenic Bacteria

CARD: The Comprehensive Antibiotic Resistance Database. A bioinformatic database of resistance genes, their products and associated phenotypes. SNPs and AMR Detection Models; Resistome predictions: 50,014 WGS assemblies

MBGD: Microbial Genome Database for Comparative Genomics

VFDB: A Database of Virulence Factors of Pathogenic Bacteria

CDC: Keeping a tab on the infectious Diseases all over the Globe; Mortality and Morbidity Weekly Report (MMWR); Emerging Infectious Diseases (EID)

Wellcome Sanger Institute: Using genome sequences to advance understanding of the biology of humans and pathogens to improve public health