GFScan: a gene family search tool at genomic DNA level.
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/.
Xuan
Zhenyu
Z
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
McCombie
W Richard
WR
Zhang
Michael Q
MQ
D000595:Amino Acid Sequence; D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D002256:Carbonic Anhydrases / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics; D016678:Genome; D020662:Guanine Nucleotide Exchange Factors; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D017434:Protein Structure, Tertiary / Q000235:genetics; D011518:Proto-Oncogene Proteins; D017981:Receptors, Neurotransmitter / Q000235:genetics; D015682:Retroviridae Proteins, Oncogenic / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014157:Transcription Factors / Q000235:genetics
D004268:DNA-Binding Proteins; D020662:Guanine Nucleotide Exchange Factors; C057811:MCF2 protein, human; C512843:Mcf2 protein, mouse; D011518:Proto-Oncogene Proteins; D017981:Receptors, Neurotransmitter; D015682:Retroviridae Proteins, Oncogenic; D014157:Transcription Factors; D004247:DNA; D002256:Carbonic Anhydrases