| ECCB 2002 Poster sorted by: Author | Number Next | Previous poster (in order of the view you have selected) |
Title: ThoR --- A Domain Discovery and Curation Tool | P28 |
Dickens, Nicholas J.; Ponting, Chris P. nicholas.dickens@anat.ox.ac.uk MRC Functional Genetics Unit, University of Oxford |
| Proteins are composed of conserved structural units that are known as domains. These domains exhibit different evolutionary heritages. The discovery and identification of these domains and their heritages is inferred from protein sequence similarities as detected from database search methods such as position-specific and iterative BLAST (PSI-BLAST) (Altschul et al., 2001) and Hidden Markhov model searches using the HMMER tools (http://hmmer.wustl.edu/). Protein sequence databases are expanding at a rapid rate, owing to the numerous genome sequencing projects reaching completion. Pfam and SMART, whose domain multiple sequence alignments are constructed using semi-automatic methods, are thus unable to update their alignments synchronously with sequences newly deposited in databases. A related problem is the identification of the set of all domain homologues that are detectable using available sequence database search methods. PSI-BLAST is the method of choice in identifying homologues with divergent sequences (Altschul et al., 2001). The poster describes a sequence database searching protocol that takes advantage of the strengths of both the PSI-BLAST and HMMER methods. The protocol is coded in the Thorough Homology Resource (THoR), this package performs exhaustive database searches and generates accurate and global multiple alignments automatically. THoR is principally a collection of sequence analysis programs and perl scripts integrated through a web-based interface run from the web server apache (http://www.apache.org/). |
| [1] Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. PMID: 11452024 |