• BH-search - an experimentally based computer search to identify unstructured membrane-binding sites in proteins.
• DNAWorks - automates the design of oligonucleotides for PCR-based gene synthesis.
• EyeBrowse - The data is now displayed as a track hub on the University of California at Santa Cruz Genome Browser
• AbDesigner - a tool for analyzing the amino acid sequence of a given protein to identify optimal immunizing peptides for production of antibodies. (NHLBI/CIT collaboration)

The following applications are only available within the NIH network.

• Robust Accurate Identification (RAId) is a suite of proteomics tools for analyzing tandem mass spectrometry data. In addition to providing accurate statistical significance assignment, RAId offers users with different modes of data analysis: database search, generation of score distribution of all possible peptides using different scoring functions (RAId, XCorr, Hyperscore, Kscore), and statistical confidence reassignment. In particular, RAId's integrated knowledge databases incorporate known single amino polymorphisms, post-translational modifications and disease information, providing dynamic information retrieval for biomedical applications. (Yu lab, NLM)
• StrucTools - calculates surfaces, B-factor plots, hydrogen bonds, and secondary structure from a PDB coordinate file or PDB ID.
• UCSC Genome Browser - a partial mirror containing the reference sequences for the human genome and working drafts for the mouse and rat genomes.
• EMBOSS-Lite - Formerly GCG-Lite, the same user-friendly web interface, updated and modified to use the EMBOSS suite of sequence analysis programs.
• Partek Flow - web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing.