UNLABELLED: Synthetic fusion proteins have shown great potential in various biotechnological and (bio)pharmaceutical applications. They usually contain more than two protein domains joined by a linker peptide sequence which is often selected intuitively or in ad hoc manner. Thus, we developed an integrated web-based system, SynLinker, to provide appropriate linker candidates for constructing fusion proteins. We compiled a total of 2260 linker sequences comprising of natural linkers extracted from a set of non-redundant multi-domain proteins in Protein Data Bank and artificial/empirical linkers collected from literature and patents. Multiple query interface allows users to search for the desired linker candidates based on selection criteria and their preferences. In addition, a selected linker can be combined with two domain structures which are uploaded and appended at its N and C terminals, thereby predicting a de novo structure of the fusion protein. Hence, SynLinker can serve as a systematic tool for researchers who are interested in designing synthetic fusion proteins. AVAILABILITY AND IMPLEMENTATION: SynLinker is freely available at http://bioinfo.bti.a-star.edu.sg/synlinker. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: Codon optimization has been widely used for designing synthetic genes to improve their expression in heterologous host organisms. However, most of the existing codon optimization tools consider a single design criterion and/or implement a rather rigid user interface to yield only one optimal sequence, which may not be the best solution. Hence, we have developed Codon Optimization OnLine (COOL), which is the first web tool that provides the multi-objective codon optimization functionality to aid systematic synthetic gene design. COOL supports a simple and flexible interface for customizing various codon optimization parameters such as codon adaptation index, individual codon usage and codon pairing. In addition, users can visualize and compare the optimal synthetic sequences with respect to various fitness measures. User-defined DNA sequences can also be compared against the COOL optimized sequences to show the extent by which the user's sequences can be further improved. AVAILABILITY AND IMPLEMENTATION: COOL is free to academic and non-commercial users and licensed to others for a fee by the National University of Singapore. Accessible at http://bioinfo.bti.a-star.edu.sg/COOL/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.