SledgeHMMER：一个用于批量搜索Pfam数据库的网络服务器。
SledgeHMMER: a web server for batch searching the Pfam database.
作者信息
Chukkapalli Giridhar, Guda Chittibabu, Subramaniam Shankar
机构信息
San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA.
出版信息
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。
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