title: SnS-Align: a graphic tool for alignment of distantly related proteins.
abstract: Genomic sequences for many animal species are now available in the public domain. Protein similarity search in evolutionarily distant organisms by sequence comparison often turns out to be difficult. Here, we present the Structure and Sequence Alignment (SnS-Align) tool that graphically presents pairwise local alignment of sandwiched protein sequences, a hybrid of the primary protein sequence and its secondary structure. The utility of the tool is demonstrated by sample analysis of the gap junction protein superfamily of innexins/pannexins and the classic myoglobin family. SnS-Align can also be used for demarcation of the structurally conserved domains within superfamilies of paralogous genes.
authors.affiliation: Department of Molecular and Microbiology, College of Science, George Mason University, PW2 University Blvd., Manassas, VA 20110, USA. gmanyam@gmu.edu
authors.forename: Ganiraju
authors.initials: G
authors.lastname: Manyam
authors.forename: Ancha
authors.initials: A
authors.lastname: Baranova
authors.forename: Mikhail
authors.initials: M
authors.lastname: Skoblov
authors.forename: Rakesh K
authors.initials: RK
authors.lastname: Mishra
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment
chemical_list: D011506:Proteins