Q: Some of the buttons and menus don't seem to work properly, why's that?

A: Be sure to have javascript enabled in your browser and to use a new browser (e.g. Netscape 7+ or Internet Explorer 5+)

Q: I wonder why the default E-value cutoff is 1x10-4 and not 10.0 ?

A: Using the lower cutoff value will display only those hits that are significant for a typical comparison of a plant gene vs. moss at peptide level. For BLASTN (not recommended) the default is 1x10-2.

Q: How do I interpret the sequence names and the contents of the sequence headers that are in my BLAST output?

A: Please read the information on the "about" page for details concerning the sequence nomenclature.

Q: How do I know which database to choose?

A: Please be sure to read the information on the "about" page as well as the documentation about databases. If unsure use the default (ppp_nr).

Q: Some time ago I did a search with the same query, now I get a different result. How can this happen?

A: As new data becomes available and/or parameters are subject to change, new versions of the clustered database will change, especially with respect to contig names and cluster contents. (please have a look at the version/release history on the "about" page)

Q: What are all those BLAST options for and how do I interpret the output?

A: Please read the NCBI BLAST tutorial.

Q: I want to BLAST against several databases with (nearly) the same options / the same sequence without filling out the whole form again each time?

Instead of the BLAST interfaces' reset button use your browsers reload button. Browsers normally cache form contents inbetween reloads (not SHIFT-reload!). This practise will convince the cosmoss server that it's a new BLAST job while conserving most of the form information for reuse. Such a submission without reload/reset of the page will cause an error, because the interface thinks the same job is submitted twice.

Q: I had a batch BLAST job running over night and when I try to access it the other morning, I can't access it or get strange errors. What's wrong?

The temporary folder where the BLAST results are stored is flushed once a week: Monday 23.15 CET. You'll have to re-run your job if this affects you, sorry!

Q: How can I access and read the articles from the PhyscomeProjectWiki and participate in the efforts around the Physcomitrella genome?

As we are in the phase of annotating the moss genome, we need your help in getting it in as good a shape as possible before its public release within the next few months. The browser and the wiki are still password-protected because the annotation process is only beginning, but all interested members of the Moss community who are serious about providing annotation contributions are welcome. To have access now, in return for help e.g. with annotation of your favorite genes, you will need to register by contacting R. Quatrano at rsq@wustl.edu for instructions on how to register and guidelines for annotation and contribution to the wiki. Visit the genome consortium page to find out more!

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