Multimotif PHIBLAST a new tool for Database Searching and Sequence Alignment.pdfVIP

Multi-motif PHI-BLAST: a new tool for Database Searching and Sequence Alignment Nitin Bhardwaj, IIT Bombay ABSTRACT The present PHI-BLAST used for searching genomic database available on the NBCI server takes only one motif as the input and so needs as many runs as the number of motifs the user has to give. And hence it cannot give any preference to any particular motif. We have developed a Multi-Motif version of PHI-BLAST, which takes multiple motifs as the input and picks up only those sequences from the database which have a minimum number of motifs given by the user allowing the user to be as specific as he/she wants to be. We have also developed some higher versions of PHI-BLAST such as the Ranked-motif PHI-BLAST which gives the higher ranked motifs a preference in the database searches. In this paper first we present the strategy and algorithm involved in these tools and later we compare the results of these tools with those from PHI-BLAST. The results are as good as the ones by PHI- BLAST or better. Keywords: Motif, Subject and Query sequence, Local and Global Alignment, PHI-BLAST ________________________________________________________________________ INTRODUCTION The sequence itself is not informative; it must be analyzed by comparative methods against existing databases to develop hypothesis concerning relatives and function. This is done by alignment, the process of lining up two or more sequences to achieve maximal levels of identity (and conservation, in the case of amino acid sequences) for the purpose of assessing the degree of similarity and the possibility of homology. Broadly there are two types of alignments: Global Alignment : The alignment of two nucleic acid or protein sequences over their entire length, such tha