Xuan Zhenyu, McCombie W Richard, Zhang Michael Q
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Genome Res. 2002 Jul;12(7):1142-9. doi: 10.1101/gr.220102.
We have developed GFScan(Gene Family Scan), a tool that identifies members of a gene family by searching genomic DNA sequences with genomic DNA motifs (or matrices) that are representative of the family. We have tested GFScan on four human gene families including the neurotransmitter-gated ion-channels (NGIC) family, the carbonic anhydrases (CA) family, the Dbl homology (DH) domain family, and the ETS-domain family. All known members of these families with motifs mapped to sequenced genomic DNA regions were found, whereas some novel genomic locations were also found to match the motifs, which may indicate new members in these families. Compared with other methods, GFScan recognized all true positives with much fewer false positives. We also showed that motifs constructed based on human genes could be used to search the mouse genome to identify orthologous family members in mouse. This program is available at http://www.cshl.org/mzhanglab/.
我们开发了GFScan（基因家族扫描）工具，该工具通过使用代表该家族的基因组DNA基序（或矩阵）搜索基因组DNA序列来识别基因家族的成员。我们已在四个人类基因家族上测试了GFScan，包括神经递质门控离子通道（NGIC）家族、碳酸酐酶（CA）家族、Dbl同源（DH）结构域家族和ETS结构域家族。这些家族中所有已知成员的基序都映射到了已测序的基因组DNA区域，同时还发现一些新的基因组位置与基序匹配，这可能表明这些家族中有新成员。与其他方法相比，GFScan识别出了所有真阳性，且假阳性要少得多。我们还表明，基于人类基因构建的基序可用于搜索小鼠基因组，以识别小鼠中的直系同源家族成员。该程序可在http://www.cshl.org/mzhanglab/获取。
