TY - JOUR
T1 - GFScan
T2 - A gene family search tool at genomic DNA level
AU - Xuan, Zhenyu
AU - McCombie, W. Richard
AU - Zhang, Michael Q.
PY - 2002
Y1 - 2002
N2 - 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/.
AB - 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/.
UR - http://www.scopus.com/inward/record.url?scp=0036068585&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0036068585&partnerID=8YFLogxK
U2 - 10.1101/gr.220102. Article published online before print in June 2002
DO - 10.1101/gr.220102. Article published online before print in June 2002
M3 - Article
C2 - 12097353
AN - SCOPUS:0036068585
SN - 1088-9051
VL - 12
SP - 1142
EP - 1149
JO - Genome Research
JF - Genome Research
IS - 7
ER -