GAS stands for Genome Annotation Search engine, it provides three types of search: Keyword search, Advanced search (SRS like), and BLAST search to help users finding the useful annotation information in our GAT database.
Type one or more words into the GAS search box. Your search will try to find all matches in either the geneid, genename, or product fields in both dots.vbigeneedit and dots.vbirnaedit table.
By default, GAS returns the wildcard search results, in which, the search item matches any part (substring) of these subject fields.
Check the 'exact match' checkbox to restrict your search: GAS will return some results only when at least one of the three subject fields are exactly the same as your search item.
To restrict your search results within one or more species, you can use the checkbox(es) to specify the genome(s) you are looking for.
(** Please notice that all searches in GAS are case insensitive **).You can make more complicated searches using the GAS advanced search (SRS like)function. First, you can search on more information fields than you can in the keyword search, using the drop down menu below the search box. Second, you can combine all of your search fields using boolean operators (and, or, and not). The full list of fields includes:
| Fields | How to use |
|---|---|
| GeneID, Gene Name, Product, User | As in the keyword search. |
| Start Postion, End Position | You can search for genes with a specific start or end position by entering a number in the input field. OR. You can search genes basing on their start, stop position ranges, eg 1..500000. |
| Gene Length, Protein Length | You can search for genes with a specific gene length or protein length by entering a number in the input field. OR. You can use ">,<,==,>=,<=,!=" operators in front of a number to search for genes basing on the range of gene length or protein length. |
| Category,SubCategory,Replicon,Annotator | Select on the right side drop down menu, you can limit your search results basing gene category, gene subcategory, replicon or level of the viewer (curator). |
To restrict your search results within one or more species, you can use the checkbox(es) to specify the genome(s) you are looking for.
The advanced searching only applies on protein coding genes (searching only the dots.vbigeneedit table).
As a complement to searching the annotations, we provide a link here to use our local BLAST server. You can use this BLAST server to find similarity in either nucleotide or protein sequences against our agrobacterium biovar genome data as well as the data in NCBI nr, nt databases.