Web-Accessible Applications

Web-Accessible Scientific Applications

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.
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.
PROSPECT - PROSPECT is a threading-based protein structure prediction system. PROSPECT will find structural homologs of a target sequence, even when the structural homolog sequences have insignificant identity to the target sequence.
Computational Molecular Biology - useful links for computational molecular biology.

BIOBASE Databases - A comprehensive portfolio of standard and customized databases, as well as analytical tools. NIH-only: requires an NIH domain username & password. These databases and tools include:

ExPlain Analysis System - promotes biological interpretation of high throughput experiments like microarrays, proteomic data, and ChIP-chip experiments. The intuitive workflow allows systematic creation of experimentally testable hypothesis for both gene transcription regulation and signalling networks.
TRANSFAC - provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signalling components.
TRANSPRO - a collection of annotated transcription start sites for human, mouse, and rat promoter sequences.
TRANSCOMPEL - a database of composite gene regulatory elements found in many promoters and enhancers.
TRANSFAC Professional - a web interface to the TRANSFAC database of eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.

TrxFacMiner - A web-based interface that uses the TRANSFAC database to report all known genes in the human genome that are near or overlap a chosen transcription activation factor binding site. (NIH-only)

Molecules R Us - 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.
Indie - creates 'movies' of molecules in gif or mpg formats. This tool has been merged with Structools.

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.

Whales (Web Homology ALErt Service) is a sequence alert service. Users define text terms or sequences of their interest, which are searched for in the new DNA/Protein sequences each week and the results returned by email.

Helix Systems Scientific Supercomputing at the NIH