This is a general out line for easy navigation in Dicty WorkBench. This is neither a documentation nor a tutorial but aimed at familiarizing this Dicty portal. Extensive documentation (FAQs) and tutorials are available for Biology WorkBench for those who never used it before. So the main focus is on Dicty pages and where to look for Dicty related stuff in Biology WorkBench.
NOTE: Certain features are still being optimized. So please follow the suggestions. Report any problems you may encounter and help us in fine tuning our tools.
BROWSER REQUIREMENTS:For best results use Netscape 4.7 or Internet Explorer 5. This will avoid frequent problems like improper displays and browser crashes especially when you expect large returns with your search.
"Browse" feature provided on main DictyWorkBench page will list all 8,000 plus ORFs and their protein names. If you have a slow Internet connection it will take a while to load this > 1MB file. So it is advisable to avoid using this and straight go to Annotation Table .
If you can load the browse list with ease you may want to sort the entire list by clicking on protein name and look for your favorites and their new friends. Then by clicking on the hyper linked ORFID you can go to the annotation table of corresponding ORF.
This annotation table lists the Protein Name (obtained from BLAST results) RPS BLAST hits etc. By clicking on the Protein Name you can search entire database for matches. Ex. You are looking at Uridine kinase. If you click on Uridine all proteins whose name contain Uridine will show up in your search. If you click on kinase all kinases will show up. This may include glucose kinase, protein kinase and some kinase phosphatase etc. Often times this may not be what you want to search for. You can use the bottom table to set up your search criteria to eliminate or include your terms of interest, with features like 'exactly equal to', 'not equal to' 'and' 'or' etc.
You will also find links to BLAST results table, PFAM domain analysis table, ORF Details (like from which contig it is coming from and related details) etc. Protein name for a given ORF is selected from protein BLAST hits with NCBI non-redundant database. The corresponding protein is listed by its GI number. You can either look at that information or import that sequence to Biology WorkBench for further analysis. RPS BLAST top hit is listed here in the table. If you want to view the alignment and complete original out put you can click on "RPS BLAST Results" link.
BLAST results and PFAM domain analysis tables were also built on similar frame and features. You can view domain alignment of a PFAM model and a given ORF by clicking "View Original PFAM Results" icon.
To work in Biology WorkBench and to import sequences from Dicty pages to Bilogy WorkBench you need to set up an account. You can import DNA or protein sequence of an interested ORF to Biology WorkBench by clicking on appropriate link from any of Dicty WorkBench tables.
Once in Biology WorkBench you will be able to BLAST your sequences against both nucleotide and protein sequences of all HMM predicted ORFs (from sanger and Jena contigs) and selected 8,000 plus sequences besides several other databases. Ex.If you are using protein tools, first select your sequence and select a tool like BlastP and then select the databases you want to search against.
I hope this general outline helps in easy navigation and formulating your searches.