IMEx-web: Imperfect Microsatellite Extraction Webserver
Webserver for extracting microsatellites from genome sequences






Welcome to IMEx Webserver

Imperfect Microsatellite Extractor (IMEx) is a tool for extracting Perfect, Imperfect and Compound Microsatelites or Simple Sequence Repeats (SSR's) or Short Tandem Repeats (STR's) from genome sequences. IMEx is an efficient, fast and user-friendly program can search for microsatellites in the way the user wants. Using IMEx, the users can:

  • search perfect microsatellites separately.
  • get the coding/non-coding information of the microsatellite tracts
  • generate alignments with consensus microsatellite tracts
  • restrict the imperfection limit for repeat unit of each size
  • set the imperfection percentage threshold of each repeat size
  • restrict the minimum number of repeat units of a tract of each size
  • search for repeats of a particular size or for all sizes
  • search for a particular pattern microsatellite tracts
  • set the flanking sequence size limit
  • standardize the repeats.
  • design primers using Primer3.

About Microsatellites

Microsatellites or Simple Sequence Repeats (SSRs) are short tandemly repeated sequence motifs consisting of 1-6 bp. Microsatellites are observed in almost all known genomes with a significant percentage and suffer higher rates of mutation than the rest of the genome. These microsatellite tracts are subjected to many kinds of modifications, such as point mutations (Substitutions, Insertions and Deletions) making the tract an 'Imperfect' microsatellite tract (Eg: GCGCGCAGCGC). Imperfect repeats are more stable (less prone to slippage mutations) than perfect repeats. Imperfect microsatellites are used in various genetic studies including DNA fingerprinting and population genetics. It is also implicated that the mutations occurring at microsatellite loci with in or near certain genes are responsible for several human neurodegerative diseases. Microsatellites are widely distributed in the genome, both in coding and in non coding regions. Microsatellites in coding regions can result changes in protein product of genes, leading to several genetic diseases such as muscular dystrophy. Repeats in non-coding regions are known to modify the protein function by effecting the gene regulation. It was also reported that microsatellite instability induces development of cancer.


Suresh B. Mudunuri and Hampapathalu. A. Nagarajaram (2007) IMEx: Imperfect Microsatellite Extractor. Bioinformatics 23(10):1181-1187.

H. A. Nagarajaram and Suresh B.Mudunuri IMEx-web: A Web server for extraction and analysis of simple sequence repeats in viral and prokaryotic genomes.(Communicated)


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