This tool is based on UNIX command grep with option -f. It matches content of one query against another. For example, assume you have two queries - one that contains EST accession numbers and some other information:

AA001229      12      12
A001501       7       7
AA001641      6       6
AA001842      6       6
AA002047      6       6
AA004638      3       3

and another that is a typical BED file describing genomic location of some ESTs:

chr7 115443235 115443809 CA947954_exon_0_0_chr7_115443236_f 0 +
chr7 115443236 115443347 DB338189_exon_0_0_chr7_115443237_f 0 +
chr7 115443347 115443768 DB338189_exon_1_0_chr7_115443348_f 0 +
chr7 115443239 115443802 AA001842_exon_0_0_chr7_115443240_f 0 +
chr7 115443243 115443347 DB331869_exon_0_0_chr7_115443244_f 0 +
chr7 115443347 115443373 DB331869_exon_1_0_chr7_115443348_f 0 +

Using this tool you will be able to tell how many ESTs in Query1 are also preset in Query2 and will output this:

chr7 115443239 115443802 AA001842_exon_0_0_chr7_115443240_f 0

if Match option is chosen.