Bioinformatics is an interdisciplinary area of research, which also plays a vital role in the field of agriculture based studies. Tools of bioinformatics provides significant role in agriculture research. Present paper is also focusing on agriculture informatics. As we know using bioinformatics tool we can explore many more hidden information from agriculture data. In this paper we had applied ...

MOTIVATION Many multiple sequence alignment tools have been developed in the past, progressing either in speed or alignment accuracy. Given the importance and wide-spread use of alignment tools, progress in both categories is a contribution to the community and has driven research in the field so far. RESULTS We introduce a graph-based extension to the consistency-based, progressive alignment...

MOTIVATION We introduce a novel approach to multiple alignment that is based on an algorithm for rapidly checking whether single matches are consistent with a partial multiple alignment. This leads to a sequence annealing algorithm, which is an incremental method for building multiple sequence alignments one match at a time. Our approach improves significantly on the standard progressive alignm...

MOTIVATION Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, C(*)1 and C(S)1, extensions of statistics for pairwise comparison of the joint k-tuple content of all the sequenc...

Multiple sequence alignments reveal patterns of conservation that can be exploited in database searches using “profile” methods. Starting with a single nematode sequence that has no informative BLAST hits, I give a real example of the use of multiple alignment and profile search software to detect informative remote homologies. It used to be that most new sequences were novel, with no informati...

BIOLOGICALLY RELEVANT MULTIPLE SEQUENCE ALIGNMENT Hyrum D. Carroll Department of Computer Science Doctor of Philosophy Researchers use multiple sequence alignment algorithms to detect conserved regions in genetic sequences and to identify drug docking sites for drug development. In this dissertation, a novel algorithm is presented for using physicochemical properties to increase the accuracy of...

In this PhD thesis the segment-based approach for multiple sequence alignment, initially introduced by the DIALIGN program, is thorougly investigated and substiantially improved. The segment-based approach belongs to the class of local alignment methods and thus is very strong in finding locally conserved motifs, whereas global methods align the input sequences globally from the beginning to en...

A program is described for simultaneously aligning two or more molecular sequences which is based on first finding common segments above a specified length and then piecing these together to maximize an alignment scoring function. Optimal as well as near-optimal alignments are found, and there is also provided a means for randomizing the given sequences for testing the statistical significance ...

We present an overview of multiple sequence alignments to outline the practical consequences for the choices among different techniques and parameters. We begin with a discussion of the scoring methods for quantifying the quality of a multiple sequence alignment, followed by a discussion of the algorithms implemented within a variety of multiple sequence alignment programs. We also discuss addi...

It is shown that the multiple alignment problem with SP-score is NP-hardforeachscoringmatrixinabroadclassM that includes most scoring matrices actually used in biological applications. The problem remains NP-hard even if sequences can only be shifted relative to each other and no internal gaps are allowed. It is also shown that there is a scoring matrix M 0 such that the multiple alignment prob...