Saturday, 20 October 2012
Multiple Sequence Alignments (MSAs) have significant role in the downstream analysis which includes identifying conserved patterns through evolution, functionally important residues, protein secondary and tertiary structure and the nsSNPs (non synonymous Single Nucleotide Polymorphisms) that have a basic role for altering a protein function. MSAs, thus, have become an active area of research in the domain of bioinformatics. A large number of MSA methods are available such as Clustalw, SATe,T-Coffe, Muscle, MAFFT, Kalign etc., but none of them is capable of producing a correct alignment for all situations. Therefore, to have knowledge of the most accurate MSA method in the initial stage of a biological research work is very essential and important which may help in choosing the right MSA method for the right situation.
Reference alignment may be constructed either based on actual data by a MSA method and then enhance its accuracy by making some editing by hand or through a simulated tool such as indel-Seq-Gen (Strope et al. 2009), Rose (Stoye et al. 1998), Simprot (Pang et al. 2005) etc. Alignment generated by a MSA method for the purpose of testing its accuracy is called test alignment. Currently, very few MSA comparing tools are available and they have also some deficiencies; firstly, they are unable to manage alignments comprising of even few thousands of sequences; secondly they have implemented one or two scoring functions to compare MSAs. Thus, they are not comprehensive tools for comparing MSAs.
You will develop ‘MQAT’ is a graphical user interface based application that will compare two or more test alignments with reference alignments using various scores such as SPS and CS etc. MQAT will display various statistics and graphs/charts of results of comparison of the alignments. MQAT will also enable a user to print results in PDF, JPEG or text form. The most notable feature of MQAT is that it can manage thousands of biological sequences. A user will be able to save all the activities performed in MQAT in XML format.
For further information abut SPS,CS and other relevant terms/concepts read the document titled as ‘Assessing Multiple Sequence Alignments Using Visual Tools’.
