RT Journal
A1 Xuan, Zhenyu
A1 McCombie, W. Richard
A1 Zhang, Michael Q.
T1 
GFScan: A Gene Family Search Tool at Genomic DNA Level
JF Genome Research 
JO Genome Research 
YR 2002 
FD July 01 
VO 12 
IS 7 
SP 1142 
OP 1149 
DO 10.1101/gr.220102 
UL http://genome.cshlp.org/content/12/7/1142.abstract 
AB We have developed GFScan (GeneFamily 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 athttp://www.cshl.org/mzhanglab/.[The following individuals and institutions kindly provided reagents, samples or unpublished information as indicated in the paper: J. Maddock and Celera Genomics.]