1. SEQUENCE UPLOAD: You may upload your DNA sequences, or their genomic coordinates in D.melanogaster (Rel 3.1), and optionally extract the homologous sequences from related fly species that we have prealigned.
   
   
2. SEQUENCE ANALYSIS:You may directly upload your DNA sequences, optionally along with their orthologs, and analyze them using Stubb or Windowfit. (See Important tips below for what these are.)
   
   
3. AUTHENTICATION:You may authenticate yourself if you want to access data/results you created on this site from a different machine (or if you have deleted your browser's cookies since).
   
   
4. PROJECT MANAGEMENT:You may manage and view projects that you created earlier on this server, e.g., delete those that you no longer need. (Projects not accessed for over two weeks are automatically deleted. You may also download your projects.)

Important tips

1. Stubb is a program for finding significant clusters of binding sites over long genomic sequences, typically tens of Kbp. This web server requires total length of analyzed sequences to be less than 100 Kbp.
2. Windowfit is a program for analyzing small enhancer-length sequences, typically ~ 1-2 Kbp long, for locations and strengths of binding sites. This web server requires each analyzed sequence to be less than 10 Kbp long.
3. Both programs can analyze two species that we align with LAGAN .
4. Data analysis is organized by projects (folders), that can contain multiple sequence files. Each sequence file can contain multiple fasta sequences (eg for all genes in a pathway) along with their orthologues in another species. A (project,sequencefile) pair uniquely identifies a data set and its associated results. If the same (project,sequencefile) pair is analyzed in multiple runs, the most recent results override earlier results.
5. Do not run more than one request at a time. This may lead to corrupted results

People and References

• Eric Siggia,   Saurabh Sinha,  Yupu Liang.
• A Probabilistic Method to Detect Regulatory Modules, Saurabh Sinha, Erik van Nimwegen, and Eric Siggia, Bioinformatics. 2003;19 Suppl 1:i292-301..
• Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila,Saurabh Sinha, Mark D. Schroeder, Ulrich Unnerstall, Ulrike Gaul and Eric Siggia, BMC Bioinformatics. 2004 Sep 9;5(1):129.
• Stubb: a program for discovery and analysis of cis-regulatory modules, Saurabh Sinha,Yupu Liang,Eric Siggia, Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W555-9.

Comments and Bug reports