[Sequence Analysis] [Gene Regulation & Pathways] [Structural Biology] [Proteomics] [Alert Services] [Utilities]

Sequence Analysis Tools

• Galaxy at Helix is a web portal to command-line tools on the Biowulf cluster. Helix login and password required.
• EMBOSS - a large collection of open source sequence analysis tools. [ see also Equivalent programs in EMBOSS and GCG]
• EMBOSS-Lite Formerly GCG-Lite, the same user-friendly web interface, updated and modified to use the EMBOSS suite of sequence analysis programs.
• Multiple Alignment Workshop. Calculate & compare a multiple sequence alignment using one or more selected algorithms.
• DNAWorks - automates the design of oligonucleotides for PCR-based gene synthesis.
• MFOLD - web interface to Michael Zuker's MFOLD program. It performs secondary structure modeling of RNA and DNA sequences. (NIH-only)
• UCSC Genome Browser - a partial mirror containing the reference sequences for the human genome and working drafts for the mouse and rat genomes.
• EyeBrowse - a variation of the UCSC Genome Browser specifically for eye tissue genes and cDNA clones, developed in collaboration with NEIBank and NEI.
• Sequence Format conversion - to convert sequences between all the most common sequence formats, like Fasta, GCG, Genbank.
• SAPS - statistical analysis of protein sequences.
• Parallel Fasta search for protein sequences.
• BH-search - an experimentally based computer search to identify unstructured membrane-binding sites in proteins.
• AbDesigner - a tool for analyzing the amino acid sequence of a given protein to identify optimal immunizing peptides for production of antibodies.
• 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.
• 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.
• Computational Molecular Biology - useful links for computational molecular biology.

Gene Regulation & Pathways

• BIOBASE Databases - The helix systems will no longer host BIOBASE or ExPlain after 8/31/2011. Users can access the online version hosted by BIOBASE through NIH ISDP by logging into the ISDP website at: http://isdp.nih.gov/isdp/version.action?prodid=161. Email ISDP at NIHISDP@mail.nih.gov to request that your data is transferred over to the new site. If you have any login issues or questions email BIOBASE at muthu.meyyappan@biobase-international.com or support@biobase-international.com.

Structural Biology Tools

• Molecules To Go - allows a search of the PDB database and displays the result as text, image or interactive structure.
• StrucTools - calculates surfaces, B-factor plots, hydrogen bonds, and secondary structure from a PDB coordinate file.
• 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.
• Indie - creates 'movies' of molecules in gif or mpg formats. This tool has been merged with Structools.
• NAMD Server - run basic molecular dynamics protocols using NAMD. NIH login and password is required.

Proteomics

• The Mascot search engine uses mass spectrometry data to identify proteins from primary sequence databases. Mascot searches on our server can be run through the web interface, or by using the Mascot daemon on your own desktop PC.
• 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.