Searching Genome Projector

After keyword is entered in the top right search field and ENTER key is pressed, number of hits in each of the views is displayed in the corresponding tabs. Pins on the maps show the location of search results, and clicking on the pins can show detailed annotations. See the documentations on each view for the contents of detailed annotations. Number of hits

Regular Expressions

You can use Regular Expressions in Genome Projector search box. For example, you can search for thr operon genes in Escherichia coli with a pattern as follows:

thr[A-Z]

When you want to search for multiple entries (i.e., OR search), for example, to search for thr operon genes and rrn operon genes, a regular expression as follows can be used.

(thr|rrn)

Sequence-based Search (BLAST)

You can search Genome Projector using sequence-based search powered by BLAST. Just like keyword search, you can simply enter a sequence (raw or FASTA format, multiple FASTA entries is allowed) in a text box after opening corresponding window by pressing the “BLAST Search” button located next to the keyword search area. The system automatically identifies whether the given sequence is a nucleotide acid or amino acid sequence, and uses appropriate programs (blastp for amino acid, blastn for nucleotide) and databases. Just like the keyword search, sequence-based search shows corresponding results in all views, and also in all organisms. So you can explore the gene conservation levels by clicking through different organisms. Search Result tab shows E-values for sequence-based search.

Search Results

A vertical strip named Search Results also appears upon searching on the right hand edge of the Genome Projector View. Clicking on this strip opens the result pane temporarily, and clicking on the arrow located at the top of this strip fully opens the result pane.

Search Result Closed

Clicking on each of the results shown in this pane moves the view so that it is centered on the selected gene, and detailed annotation is shown. On the top part of this result pane are two functions:

  1. Link to this search result
  2. Download search result

Both of the functions opens up a new window, where the first shows a unique link for showing the current view searched with the current keyword. This URL can be used to share the search results among other scientists. The second link produces a tab-delimited text file containing all annotations for the search result. See here for the column definitions.

Search Result Opened

searching_genome_projector.txt · Last modified: 2009/04/19 15:41 (external edit)