MICAS: Microsatellite Analysis Server

MICAS is an interactive user-friendly web-based analysis server to find non-redundant microsatellites of a selected bacterial or archeal genome sequence. MICAS has been connected to the database MICdb3.0 that hosts microsatellites extracted from more than 5000 published prokaryotic genome sequences. The extraction of microsatellites is done using the software tool Imperfect Microsatellite Extractor (IMEx) (Suresh Mudunuri and Nagarajaram HA, Bioinformatics, 2007). All the sequenced prokaryotic genomes have been submitted to IMEx to extract all perfect microsatellites of size >=6bp and the respective repeat information has been stored in the database MICdb3.0.

What are Microsatellites?

Microsatellites, also known as Simple Sequence Repeats (SSRs) or Short Tandem Repeats (STRs) are tandem repetitions of short nucleotide motifs (ATTG, CAG, CT, A etc.) of size 1bp to 6bp. These repeats are ubiquitous in nature and are found in the genomes of all organisms including plants, animals, bacteria and viruses. They are known to be highly polymorphic, making them interesting elements of study. Microsatellites are widely used in various fields and applications such as DNA Fingerprinting, Forensics, Evolutionary Studies, Paternity Studies, Linkage Analysis, etc. Recent studies revelaed that microsatellites in bacteria are known to play an important role in adaptation in host environments.

Earlier Versions

  • MICdb 1.0: 83 Sequences.
  • MICdb 2.0: 487 Sequences.
  • MICdb 3.0: 5,043 Sequences.

MICdb3.0 is the current & latest version of the database. The database hosts the microsatellite data of 4,772 bacterial and 271 archeal genome sequences (including plasmid sequences).

Improvements in MICdb 3.0 & MICAS 3.0

  • 5,000+ Prokaryotic Sequences.
  • Graphical Representation of Results.
  • Option to Export Output Files in Various Formats.
  • Automatic & Direct Update of Genomes & SSRs from NCBI.
  • Option for Pair-wise Comparison of Genomes with regard to Microsatellite Distribution.
  • Advanced Search: Filter Repeats based on user's search criteria.

Related Publications

  • Suresh B. Mudunuri, Sujan Patnana, and Nagarajaram H.A. (2014) MICdb 3.0: Comprehensive Repository of All Bacterial Microsatellites. Database, Vol. 2014, Article ID: bau005. [Link to Paper]
  • Suresh B. Mudunuri, Appa Rao Allam, Pallamsetty S, Priyatosh Mishra, and Nagarajaram H.A. (2009) VMD: Viral Microsatellite Database - A Comprehensive Resource of All Viral Microsatellites. Journal of Computer Science & Systems Biology, vol. 2, no. 6, pp. 283-286.[Cited by 8]
  • Suresh B. Mudunuri and H. A. Nagarajaram (2007) IMEx: Imperfect Microsatellite Extractor. Bioinformatics, vol. 23, pp. 1181-1187. [Cited by 66]
  • V. B. Sreenu, Vishwanath Alevoor, J. Nagaraju and H. A. Nagarajaram (2003). MICdb: Database of Prokaryotic Microsatellites. Nucleic Acids Research 31:106-108. [Cited by 34]
  • V. B. Sreenu, G.Ranjitkumar, S.Swaminathan, S.Priya, B.Bose, M.N.Pavan, Geetha Thanu, J.Nagaraju and H.A.Nagarajaram (2003) MICAS: A fully automated web server for microsatellite extraction and analysis from prokaryote and viral genomic sequences. Applied Bioinformatics 2(3) 165-168.[Cited by 11]