直接iprscan是不行的,需要加个-cli才能正常运行,不然出现一大堆HTML的代码,这里的cli 是command-line interface 简写。

usage: ./iprscan -cli [-email <addr>] [-appl <name> ...] [-nocrc] [-altjobs] [-seqtype p|n] [-trlen <N>] [-trtable                                                                                             <table>]
              [-iprlookup] [-goterms] -i <seqfile> [-o <output file>]

 -i <seqfile>      Your sequence file (mandatory).
 -o <output file>  The output file where to write results (optional), default is STDOUT.
 -email <addr>     Submitter email address (required for non-interactive).
 -appl <name>      Application(s) to run (optional), default is all.
                   Possible values (dependent on set-up):
 -nocrc            Don't perform CRC64 check, default is on.
 -altjobs          Launch jobs alternatively, chunk after chunk. Default is off.
 -seqtype <type>   Sequence type: n for DNA/RNA, p for protein (default).
 -trlen <n>        Transcript length threshold (20-150).
 -trtable <table>  Codon table number.
 -goterms          Show GO terms if iprlookup option is also given.
 -iprlookup        Switch on the InterPro lookup for results.
 -format <format>  Output results format (raw, txt, html, xml(default), ebixml(EBI header on top of xml), gff)
 -verbose          Print messages during run

-appl 就是你想用的数据库,默认情况下是所有数据库都搜索,但是,比如我只想用pfam数据库,就可以"-appl hmmpfam", 如果你希望使用多个指定数据库,就多用几次-appl,例如“-appl hmmpfam -appl profilescan"
-iprlookup 会给出IPR自己的domain编号,例如IPR008237
currently, InterPro does not store match information for the optional algorithms TMHMM or SignalP. Therefore, if you search a sequence using InterProScan and do not specify the "-nocrc" option (to force searching without doing the CRC calculation and look-up), only the matches that are in the InterPro database will returned and these will NOT include predictions from TMHMM or SignalP. Currently, InterProScan is unable to search these separately but we are working on a solution.
大意是如果使用默认参数,那些在数据里已有的蛋白,其TMHMM or SignalP的结果不会被报告,可能是数据库的license的问题,而且iprscan还无法单独进行TMHMM or SignalP的搜索以补充缺失的结果。

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