The Triplex-forming Oligonucleotide Target Sequence Search engine was developed to facilitate the use of TFOs in gene-specific manipulation of human and mouse DNA. A web form gathers search criteria from the user, including the gene and species to be searched, the minimum percent G and maximum number of pyrimidine interruptions allowed in the TFO target sequence, the minimum target sequence length, and the length of promoter region to be searched. The user is also given the option choose whether to search a raw genomic sequence or a repeat-masked genomic sequence. The engine searches both strands of the gene sequence for purine runs, allowing non-contiguous pyrimidine interruptions. Search results are returned in a web page listing the found TFO target sequences along with descriptive information about them, including length, percent G, position on the chromosome, gene region in which they were found, matches to known repeat sequences, and PubMed identifiers for articles reporting validated TFO target sequences. The search results are enriched with links to NCBI resources: Entrez Gene, GenBank, BLAST, and PubMed
The TFO target sequence search is executed on the NCBI assembled chromosome sequence data. Gene and gene region locations on chromosome sequences are derived from the NCBI Map Viewer sequence-to-gene mapping data, using NCBI Reference mapping data for human and mouse genes. Gene symbols and descriptions are from the NCBI Entrez Gene data.
Repeat sequence masking is performed with the RepeatMasker software in conjunction with WU BLAST sequence alignment software and Repbase Update repeat sequence data. In cases where the user chooses to search raw genomic sequence data rather than repeat-masked data the Repbase Update data are used to flag exact matches of TFO target sequences within known repeat sequences.
PubMed identifiers in the search results are from a literature search performed by us.
Versions and release dates for source data are:
NCBI Human Genome Build 36.2, September 2006 (assembled chromosome and mapping data)
NCBI Mouse Genome Build 36.1, May 2006 (C57BL/6J assembled chromosome and mapping data)
NCBI Entrez Gene 10-9-2006 (searchable list of gene names and descriptions)
RepBase Update Volume 11, Issue 1, 3-14-2006 (repeat sequence masking)
RepBase Update Volume 11, Issue 9, 10-4-2006 (repeat flag data)
If you use this search engine in your work please cite Oligonucleotides 16:196-201 (2006).