Hi, I am not so expert in programming. I have some protein families. I want to create a local HMMER like webserver/tool and implement hmmsearch in it. Please suggest me how can I implement this?
Do you really need the tool to be web accessible? HMMER3 is completely runable from the command line. You simply need to download it and install it. Otherwise all a website is in this case is a front-end for providing data, setting options, passing them to the command-line tool, and then reading the results back and displaying them. In which case I would recommend reading some basic web-building tutorials.
Here are a few examples of questions on stackoverflow with people wanting to build relatively simple web interfaces to python scripts, etc:
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I am looking for interface something like http://pdslab.biochem.iisc.ernet.in/cgi-bin/HMM.cgi but this one gives not the nice results.
Like I said, there is nothing special about implementing a web interface. If you need users to be able to use it is is certainly convenient. You'll need to do some reading and practicing about writing basic web-pages, in particular using forms, check boxes, etc to send what would normally be command-line parameters and data to the program. Then running the program and parsing the results.