title: Spial: analysis of subtype-specific features in multiple sequence alignments of proteins.
abstract: BACKGROUND
  Spial (Specificity in alignments) is a tool for the comparative analysis of two alignments of evolutionarily related sequences that differ in their function, such as two receptor subtypes. It highlights functionally important residues that are either specific to one of the two alignments or conserved across both alignments. It permits visualization of this information in three complementary ways: by colour-coding alignment positions, by sequence logos and optionally by colour-coding the residues of a protein structure provided by the user. This can aid in the detection of residues that are involved in the subtype-specific interaction with a ligand, other proteins or nucleic acids. Spial may also be used to detect residues that may be post-translationally modified in one of the two sets of sequences.
  
  
  BACKGROUND
  http://www.mrc-lmb.cam.ac.uk/genomes/spial/; supplementary information is available at http://www.mrc-lmb.cam.ac.uk/genomes/spial/help.html.
authors.affiliation: Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 1TP, UK.
authors.forename: Arthur
authors.initials: A
authors.lastname: Wuster
authors.forename: A J
authors.initials: AJ
authors.lastname: Venkatakrishnan
authors.forename: Gebhard F X
authors.initials: GF
authors.lastname: Schertler
authors.forename: M Madan
authors.initials: MM
authors.lastname: Babu
mesh_terms: D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins