SledgeHMMER: A web server for batch searching the Pfam database

Giridhar Chukkapalli, Chittibabu Guda, Shankar Subramaniam

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

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 (∼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.

Original languageEnglish (US)
Pages (from-to)W542-W544
JournalNucleic acids research
Volume32
Issue numberWEB SERVER ISS.
DOIs
StatePublished - Jul 1 2004

ASJC Scopus subject areas

  • Genetics

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