BACFinder can be queried by Rat Gene Symbol (for example: Bfsp1), GenBank sequence ID (for example: AB000778) or by BAC ID (for example: gvuh). A combination of more than one field can be used.

Depending on what kind of query being made one of two different styles of result pages appear when you hit the "Send Request" button.

If you search for gene name or GenBank ID the result looks as follows:

In the example above entering the gene Bfsp1 (Genbank ID AB003104) will generate a page where the query sequence is seen on a blue colored background at the top. Below you find the label gime (referring to a BAC sequence) on a pink background and below that, on an orange background, a double line representing the alignment between part of the query sequence (AB003104) and the subject sequence (a BAC labeled gime and a sequencing run labeled AS). There are several alignments between AB003104 and this BAC and each of these alignments is represented by a double line (yellow background). The reason for these multiple alignments is that the AB003104 sequence is a cDNA sequence but since the intron sequences are present in the BAC sequences the alignment becomes interrupted. As a result each alignment displayed indicates the positions of an exon in the Bfsp1 gene and so it becomes relatively simple to put together the exon/intron structure of this gene.

Please note that the orange/yellow colors are just there to separate the different alignments and carry no information by itself. Note that the size of the alignment is indicated at the right of the double line and that the position of the double line is placed according to its basepair position in the query sequence.

The next pink background indicates the alignment of AB003104 against another BAC labeled gvre.

The table below presents the same data as in the figure above. To the left on green background the GenBank ID of the query sequence is displayed. The text on blue background refers to BAC symbols and runs. The data on pink background describes the alignement start and stop position on the AB003104 query sequence. Consider, for instance, the alignment between AB003104 and BAC gimeAS. Here the alignment is between position 1033 and 1317 on AB003104, which is the same as a 284 bp alignment (1317-1033=284). Taking a look in the figure above you see the text gimeAS 284 bp close to the alignment, presenting the same information.

In addition, E-value and percentage sequence similarity is given and the individual alignments can be viewed by clicking on the "view" button to the right.

In case BAC accession number was search, the result show will as follows:

In this case, it must be noticed that, every blue line, represents a different run of the same BAC. Every time the result line changes tonality, means that the sequence aligned has changed, and in this case, the number next to the name of the sequence is the length of the alignment.