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70 Seema TRIVEDI Primmer CR, Raudsepp T, Chowdhary BP, Moller AP and Ellegren H. Low frequency of microsatellites in the avian genome. Genome Res. 7: 471-482, 1997. Rocha EP, Blanchard A. Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution. Nucleic Acids Res. 30(9): 2031-42, 2002. Simmons WL and Dybvig K. Biofilms protect Mycoplasma pulmonis cells from lytic effects of complement and gramicidin. Infect Immun. 75(8): 3696-9, 2007. Sluijter M, Spuesens EB, Hartwig NG, van Rossum AM and Vink C. The Mycoplasma pneumoniae MPN490 and Mycoplasma genitalium MG339 genes encode reca homologs that promote homologous DNA strand exchange. Infect Immun. 77(11): 4905- 11, 2009. Toth G, Gaspari Z and Jurka J. Microsatellites in different eukaryo tic genomes: survey and analysis. Genome Res. 10: 967-981, 2000. Trivedi S. Comparison of simple sequence repeats in 19 Archaea. Genet Mol Res. 5(4): 741-72, 2006. Trivedi S. Do Microsatellites Have Biased Associations? The Nucleus. 46(1,2): 61-76, 2003. Trivedi S. Microsatellites (SSRs): Puzzles within puzzle. Indian J Biotech. 3: 331-347, 2004.
Journal of Cell and Molecular Biology 7(2) & 8(1): 71-72, 2010 Software Review Haliç University, Printed in Turkey. http://jcmb.halic.edu.tr Tcoffee ©: Multipurpose sequence alignments program Authors: C. NOTREDAME, L. HOLME D.G. HIGGINS, J. HERINGA, O. O'SULLIVAN, K SUHRE, C. ABERGEL License: Open source freeware Tcoffee at a glance T-Coffee stands for Tree based Consistency Objective Function for Alignment Evaluation. It is a recent program for making multiple sequence alignments. It yields more accurate alignments at the cost of a slightly longer running time than other programs. Although it uses a progressive alignment method like ClustalW, it compares segments across the entire sequence set, which means aligning all the sequences at the same time. The main difference between Tcoffee and ClustalW is that Tcoffee doesn’t directly use substitution matrices to align sequences. It has many different applications and modules such as the main EXPRESSO for aligning sequences and structures, CORE for evaluating the accuracy of an alignment, Mcoffee for combining many alternative multiple sequence alignments into one. Briefly, Tcoffee could be described as a collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA and protein sequences and structures. Tcoffee and its contribution to research Recently, many researchers in the field of molecular biology have used Tcoffee modules in building, computing, evaluating and manipulating multiple sequence alignments during their original research. Although Tcoffee has been produced and developed few years ago, it has been cited in many peer reviewed articles. However the number of citations is still not comparable to ClustalW. Beside its quick ability to produce results, the open source freeware license and its efficient multifunctional modules make Tcoffee one of the most useful programs for making multiple sequence alignments. Advantages and disadvantages of Tcoffee Advantages - It produces more accurate alignments than the other methods. - It is equipped with many different tools and modules such as CORE, Mcoffee and - EXPRESSO for structure alignment, evaluation and combining alignments. Tcoffee can deal with many input formats, including FASTA, Swiss-Prot and PIR (Protein Information Resource). - Tcoffee produces sequence alignment in various formats so that it can be used as an input for another program. It also produces a colorized alignment where every residue appears on a background that indicates the quality of this alignment in (.html) and (.pdf) format. - It can produce true phylogenetic tree in Newick format by using the Neighbor Joining method. - It can work with list of DNA, RNA or protein sequences. - Tcoffee can evaluate the quality of any multiple sequence alignments using CORE server. Disadvantages - It takes longer time to align multiple sequences than other programs. - It has been cited in limited number of peer reviewed journals compared to ClustalW. However, this number is increasing rapidly every day.
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