title: SledgeHMMER: a web server for batch searching the Pfam database.
abstract: The SledgeHMMER web server is intended for genome-scale searching of the Pfam database without having to install this database and the HMMER software locally. The server implements a parallelized version of hmmpfam, the program used for searching the Pfam HMM database. Pfam search results have been calculated for the entire Swiss-Prot and TrEmbl database sequences (approximately 1.2 million) on 256 processors of IA64-based teragrid machines. The Pfam database can be searched in local, glocal or merged mode, using either gathering or E-value thresholds. Query sequences are first matched against the pre-calculated entries to retrieve results, and those without matches are processed through a new search process. Results are emailed in a space-delimited tabular format upon completion of the search. While most other Pfam-searching web servers set a limit of one sequence per query, this server processes batch sequences with no limit on the number of input sequences. The web server and downloadable data are accessible from http://SledgeHmmer.sdsc.edu.
authors.affiliation: San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA.
authors.forename: Giridhar
authors.initials: G
authors.lastname: Chukkapalli
authors.forename: Chittibabu
authors.initials: C
authors.lastname: Guda
authors.forename: Shankar
authors.initials: S
authors.lastname: Subramaniam
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D020407:Internet; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein; D012984:Software; D012985:Software Design