Help on the information displayed in GeneNest

How to access GeneNest databases?

You can go to the clusters directly via the GeneNest on page using the "Quick Search". The following searches can be performed: Use an empty query string to go to the first cluster in a database. For more search options use the "Complex Search Form"

Detailed searches

On the Complex Search Form you have several options to search against a GeneNest database. You can search with: Except for annotation search or blast you can seperate several queries by comma and the results are combined using OR. The annotation field may use Regular Expressions using the special symbols `$', `^', ` * ', `[', `]', `|', `(', `)', `!', and `\'.

Visualization of a cluster

The information for a cluster as well as some further analysis are displayed in a graphical overview. a cluster of highly similar sequences might fall apart into different contigs during the procedure of assembly (see General help on EST clustering ).

Usually you can obtain some more information about the element by moving with the mouse over the element. By clicking to an element you usually link to a new page with information about the object.

View Example


Clone Extends

A cDNA clone might have several EST sequences. if these sequences are not linked together by sequence overlap they might fall into different clusters or contigs of the same cluster. ESTs within the same cluster belonging to the same clone are connected in the graphical display and a virtual sequence of the complete clone is computed. Clones which have ESTs in other clusters or contigs are extended towards the end of the consensus and a tag is put at the end which links to the other contig or cluster.

Extends in other clusters can mean that these clusters should belong to the same Gene but the sequence information of the ESTs is to short to detect overlap. Or it might be a sign that the clone sequences are concatenated and belong to different genes.


Further questions - Feedback

Tim Beissbarth - Last Change: 7.03.00