GFScan: A gene family search tool at genomic DNA level

Xuan, Z., McCombie, W. R., Zhang, M. Q. (2002) GFScan: A gene family search tool at genomic DNA level. Genome Research, 12 (7). pp. 1142-1149. ISSN 10889051 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/12097353
DOI: 10.1101/gr.220102

Abstract

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/.

Item Type: Paper
Uncontrolled Keywords: carbonate dehydratase genomic DNA ion channel neurotransmitter article computer program controlled study DNA binding motif DNA sequence gene identification gene mapping medical research methodology mouse multigene family nonhuman priority journal protein domain sequence homology Amino Acid Sequence Animals Base Composition Base Sequence Carbonic Anhydrases Computational Biology DNA DNA-Binding Proteins Genome Guanine Nucleotide Exchange Factors Humans Mice Molecular Sequence Data Protein Structure, Tertiary Proto-Oncogene Proteins Receptors, Neurotransmitter Retroviridae Proteins, Oncogenic Sequence Homology, Nucleic Acid Software Transcription Factors
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > McCombie lab
CSHL labs > Zhang lab
Depositing User: Matt Covey
Date Deposited: 25 Apr 2013 16:45
Last Modified: 25 Apr 2013 16:45
PMCID: PMC186623
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28220

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