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


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

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

ASJC Scopus subject areas

  • Genetics

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