Chukkapalli Giridhar, Guda Chittibabu, Subramaniam Shankar
San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W542-4. doi: 10.1093/nar/gkh395.
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.
SledgeHMMER网络服务器旨在对Pfam数据库进行全基因组规模的搜索，而无需在本地安装该数据库和HMMER软件。该服务器实现了hmmpfam的并行版本，hmmpfam是用于搜索Pfam HMM数据库的程序。已在基于IA64的万亿次网格计算机的256个处理器上，针对整个Swiss-Prot和TrEmbl数据库序列（约120万条）计算了Pfam搜索结果。可以使用收集阈值或E值阈值，以本地、全局或合并模式搜索Pfam数据库。查询序列首先与预先计算的条目进行匹配以检索结果，而那些没有匹配项的序列则通过新的搜索过程进行处理。搜索完成后，结果将以空格分隔的表格格式通过电子邮件发送。虽然大多数其他搜索Pfam的网络服务器将每个查询的序列限制设为一个，但该服务器可处理批量序列，对输入序列的数量没有限制。可从http://SledgeHmmer.sdsc.edu访问该网络服务器和可下载数据。
