This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Multiseq (www.ks.uiuc.edu/Research/vmd/plugins/multiseq/) is a VMD plug-in that provides an environment for the analysis of bioinformatic data, both structure and sequence based. Structures can be loaded into Multiseq using the VMD capabilities, including direct loading of PDB structures over the Internet. Sequence data can be read in by Multiseq in either FASTA or CLUSTALW file formats. It can also use a locally installed version of BLAST [181] to search a local sequence database using a single sequence, a profile of sequences, or a fragment of a sequence or profile, including interative searches using PSI-BLAST. Various sorts of metadata can be automatically imported through the Internet, such as taxonomy information. Structures are aligned with a version of STAMP [182], which has been modified for use with RNA and to better align end regions, whereas sequence alignments are performed with CLUSTALW [183]. Since structures are generally more conserved than sequences, a particularly useful feature is the possibility of passing a structural alignment to CLUSTALWas a profile to seed the sequence alignment. The sequence alignment can also be manually edited as necessary. In order to eliminate biases present in various databases, both sequence [184] and structure [185] QR algorithms are implemented in Multiseq, which allow one to easily obtain a non-redundant data set that is suitable for evolutionary analysis. Distance based phylogenetic trees can be generated for structural similarity using QH [186] with unweighted pair group method with arithmetic averages (UPGMA) [187] and for sequence similarity using the Dayhoff PAM matrices [188] with the neighbor-joining method within CLUSTALW [183]. Multiseq is a very powerful environment to perform sequence and structural analysis in an evolutionary framework, providing valuable insights in biomedical research. All of the aforementioned features are implemented in the new version of Multiseq, of which the release is planned for the summer of 2006.
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