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Matthew McNaughton is working on the very difficult problem of multiple sequence alignment . Multiple probing of two of the chromosomes demonstrated that the pattern of allele loss is the same for both arms of the chromosome , as well as multiple sequences on the same arm of a chromosome . Three sequence analysis problems are of particular interest to us : whole-genome DNA sequence alignment , whole-genome shotgun sequence assembly , and multiple sequence alignment . The interaction data has been incorporated into Pfam to allow investigation of potentially interacting sequences and the visualisation of interacting residues within a multiple sequence alignment . The output is either a report on the matches , a multiple sequence file containing all matching patterns ( in Pearson format ) , or a multiple sequence file containing all matching pattern instances .