HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites.
HTPSELEX is a public database providing access to primary and derived data from high-throughput SELEX experiments aimed at characterizing the binding specificity of transcription factors. The resource is primarily intended to serve computational biologists interested in building models of transcription factor binding sites from large sets of binding sequences. The guiding principle is to make available all information that is relevant for this purpose. For each experiment, we try to provide accurate information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, assembled clone sequences (concatemers) and complete sets of in vitro selected protein-binding tags. In addition, we offer in-house derived binding sites models. HTPSELEX also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols. The FTP site contains the trace archives and database flatfiles. The web server offers user-friendly interfaces for viewing individual entries and quality-controlled download of SELEX sequence libraries according to a user-defined sequencing quality threshold. HTPSELEX is available from ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex/ and http://www.isrec.isb-sib.ch/htpselex.
Jagannathan
Vidhya
V
Swiss Institute for Experimental Cancer Research and Swiss Institute of Bioinformatics, Ch. des Boveresses 155, CH-1066 Epalinges, Switzerland.
Roulet
Emmanuelle
E
Delorenzi
Mauro
M
Bucher
Philipp
P
D001665:Binding Sites; D019295:Computational Biology; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D030561:Databases, Nucleic Acid; D020407:Internet; D012045:Regulatory Sequences, Nucleic Acid; D052156:SELEX Aptamer Technique; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
D014157:Transcription Factors; D004247:DNA