EPD's 40th Anniversary Symposium is open for registration !!! (click here)
(taking place in Geneva on Sep 4 2026, just after
ECCB 2026,
for more information, see https://epd.expasy.org/EPD_symposium2026/)
FindM quick guide
This page is intended as a very quick guide to FindM, one of the tools of the Signal Search Analysis Server. Comprehensive instructions can be found here.
Overview
FindM is a tool that finds the occurrences of predefined motifs in a set of DNA sequences aligned with respect to a functional site (e.g. a transcription start site). For example it can extract all promoters that contain a TATA-box.
How-to
1. Select the input
Inputs can be one of the available data sets, a user provided FASTA file or a users' FPS file.
2. Select the motif
A motif can be selected from the available libraries, a user provided Position Weight Matrix or a consensus sequence.
3. Select additional parameters
Sequence range: is the range around the functional site that FindM scans for the motif
Sequence Selection: output can be restricted to sequences with or without a match, all matches, best matches, etc...
4. Get the results
FindM output: in this example all the sequences with a TATA-box (in the region -99 to 100)