SledgeHMMER: A web server for batch searching the Pfam database

Giridhar Chukkapalli, Chittibabu Guda, Shankar Subramaniam

Research output: Contribution to journalArticle

22 Citations (Scopus)

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

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Databases
Software
Genome

ASJC Scopus subject areas

  • Genetics

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SledgeHMMER : A web server for batch searching the Pfam database. / Chukkapalli, Giridhar; Guda, Chittibabu; Subramaniam, Shankar.

In: Nucleic acids research, Vol. 32, No. WEB SERVER ISS., 01.07.2004, p. W542-W544.

Research output: Contribution to journalArticle

Chukkapalli, G, Guda, C & Subramaniam, S 2004, 'SledgeHMMER: A web server for batch searching the Pfam database', Nucleic acids research, vol. 32, no. WEB SERVER ISS., pp. W542-W544. https://doi.org/10.1093/nar/gkh395
Chukkapalli, Giridhar ; Guda, Chittibabu ; Subramaniam, Shankar. / SledgeHMMER : A web server for batch searching the Pfam database. In: Nucleic acids research. 2004 ; Vol. 32, No. WEB SERVER ISS. pp. W542-W544.
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