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

Sequence Analysis Tools

• 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.
• 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.

Gene Regulation & Pathways

• BIOBASE Databases - A comprehensive portfolio of standard and customized databases, as well as analytical tools. NIH-only: requires an NIH domain username & password. Also requires a connection to the NIH network, either directly or through VPN. These databases and tools include:
  
  
• • Biobase Knowledge Library (TRANSFAC, TRANSPATH and PROTEOME) - easily accessible, up-to-date gene, protein or disease information that has been expertly curated from the published literature. Using the BioKnowledge Retriever tool, researchers can easily access comprehensive data and retrieve sets of relevant proteins based on their characteristics. BKL Mammalian plus ExPlain offers disease-related information presented in three categories: Biomarker, Therapeutic Target, and Molecular Mechanism. BKL signal transduction information is both detailed and comprehensive, providing step by step interaction details, pathway building capabilities, and pre-drawn canonical maps.
    
    
  • 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.
    
    
• 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)
  
  

Structural Biology Tools

• 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.

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.

Alert Services

• 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.