AliBaba2.1 Prediction of transcription factor binding sites by constructing  matrices on the fly from TRANSFAC 4.0 sites.  Paste pure sequence without header or simple fasta format for  multiple sequences (>seqname).

PARAMETERS Pairsim to known sites 36 (lazy) 50 64 Mat. width in bp 10 12 Min num of sites 3 45 Min mat. conservation 70% (low) 75%80% (high) Sim. of seq to mat. 100% (matrix = seq)  1%  Factor class level 3 (e.g. RAR) 4 (e.g. RAR-b') 5 (e.g. RAR-b'1) Optional: Search only one factor  (e.g. T00820)  Search only one class  (e.g. 4.3.2.0.)  Position offset in bp (e.g. 300)  Output format seq list INFO Version 2.1 is from January 2000, modified 17.2.2000. What is it ? Documentation Samples for testing: Promoters and Exons

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(C) Niels Grabe