SledgeHMMER: a web server for batch searching the Pfam database

Giridhar Chukkapalli; Chittibabu Guda; Shankar Subramaniam

doi:10.1093/nar/gkh395

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.

Keywords

Web serverComputer scienceSequence databaseBiological databaseDatabaseSoftwareUniProtInformation retrievalServerWeb serviceBiologyData miningWorld Wide WebBioinformaticsThe InternetGenetics

MeSH Terms

AlgorithmsDatabasesProteinInternetProtein StructureTertiarySequence AnalysisProteinSoftwareSoftware Design

Affiliated Institutions

University of California, San Diego US

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Publication Info

Year: 2004
Type: article
Volume: 32
Issue: Web Server
Pages: W542-W544
Citations: 29
Access: Closed

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APA Style

                            
                                    Giridhar Chukkapalli, 
                                
                                    Chittibabu Guda, 
                                
                                    Shankar Subramaniam
                                
                            (2004). 
                            SledgeHMMER: a web server for batch searching the Pfam database. 
                            Nucleic Acids Research
                            , 32
                            (Web Server)
                            , W542-W544.
                            https://doi.org/10.1093/nar/gkh395

Identifiers

DOI: 10.1093/nar/gkh395
PMID: 15215445
PMCID: PMC441533

Data Quality

Data completeness: 86%