Hi All,
I want to use F-Match for identifying statistically overrepresented Transcription Factor Binding Sites (TFBS) in a set of sequences compared against a control set, assuming a binomial distribution of TFBS frequency. Therefore I need outputfiles from the program Match. My question is: Does anyone know how to save the results of match?
F-Match and Match are both available here
Thanks in forehand!
2 answers
In the output window there is a button to download the result which will output a .out file in text format. It is somewhere right on top. The download is formatted using spaces and can be a nightmare to parse.
Alternatively, if you have download access for the database you can download the match binaries and run them locally in which case it provides a '|' delimited output which contains the same information as their online version but is much easier to parse if you are trying to do any downstream analysis.
There is one free implementation of the MATCH algorithm at http://www.bioinf.uni-leipzig.de/Software/pwmatch/
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It's unfortunate that (1) Match can only be used via the website and (2) this requires registration and login. People are not going to create an account just to answer your query, so you'll have to hope that someone here uses those services already. Otherwise, I suggest using a freely-available alternative that we can all access without restriction.