TESS web tool

http://cbil.upenn.edu/cgi-bin/tess/tess/

TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest.

RepeatMasker

 

RepeatMasker

 RepeatMasker http://www.repeatmasker.org/ is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by the program cross_match, an efficient implementation of the Smith-Waterman-Gotoh algorithm developed by Phil Green.  

Galaxy tool

Use this site to access popular sources of data like the UCSC Table Browser. Run analyses right on the spot using a variety of integrated tools. Your results are always available and can be easily shared with others.

Galaxy is a framework for computational tools. It's great for scientists who need to use the same command line tools over and over again and want to keep a simple history of what they did with their data. By creating an account, your history will be saved indefinitely and results can be shared with other people on the same server.