SledgeHMMER: a web server for batch searching the Pfam database | Zendy

Giridhar Chukkapalli | Zendy; Chittibabu Guda | Zendy; Shankar Subramaniam | Zendy

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SledgeHMMER: a web server for batch searching the Pfam database

Author(s) -

Giridhar Chukkapalli,

Chittibabu Guda,

Shankar Subramaniam

Publication year - 2004

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkh395

Subject(s) - web server , computer science , sequence database , biological database , database , software , uniprot , information retrieval , server , web service , biology , data mining , world wide web , bioinformatics , the internet , genetics , gene , programming language

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.

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