TFBS finding in whole genome

Question

[reza]

i want to identify TFBS of camel whole genome (sequenced by illumina hiseq technology) my question is which software (windows version or web-based software) can help me to reaching my goal?

Answer 1

[EagleEye]

Check these source,

http://www.ncbi.nlm.nih.gov/genome/annotation_euk/Camelus_bactrianus/100/

http://www.ncbi.nlm.nih.gov/genome/annotation_euk/Camelus_dromedarius/100/

http://www.ncbi.nlm.nih.gov/genome/annotation_euk/Camelus_ferus/100/

PROMO might be useful for prediction of TFBS,

http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3

If it is for whole genome better to look for command line based tools rather than windows/interface or web based tools.

Answer 2

[Ian]

If you want online tools try RSAT.

Look under "Pattern matching" for the scanning of motifs using strings of ACTG and ambiguity IUPAC codes.