NIH HPC Systems: Web-based Applications
- BH-search - an experimentally based computer search to identify unstructured membrane-binding sites in proteins.
- StrucTools - calculates surfaces, B-factor plots, hydrogen bonds, and secondary structure from a PDB coordinate file or PDB ID.
- EMBOSS Explorer - a graphical user interface to the EMBOSS suite of bioinformatics tools.
- DNAWorks - automates the design of oligonucleotides for PCR-based gene synthesis.
- EyeBrowse - a variation of the UCSC Genome Browser specifically for eye tissue genes and cDNA clones, developed in collaboration with NEIBank and NEI.
- 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)
- Conditional Allele Mouse Planner (CAMP) - facilitates the planning and design of breeding strategies for generation of conditional knockout mice. CAMP provides an estimate of the number of breeders, amount of time, and costs associated with generating mice of a particular genotype. (NHLBI/CIT collaboration)
- Temporal Pattern Mining (TPM) - clusters any time-series data set, specifically iTRAQ LC-MS/MS data sets. The data points that have a similar behavior over the time course are clustered together.
- PhosSA Phosphorylation Site Assignment Algorithm for Mass Spectrometry Data. (Knepper lab, NHLBI)
- CPhos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites (Knepper lab, NHLBI)
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)
- 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.
- ΔΔGUI - a user-friendly interface to functions of the Rosetta macromolecular modeling suite for evaluating the effect of mutations on the stability of a single protein or a protein-protein complex.
- Partek Flow - web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing.