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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)

Last update May 2017