I have attached a description of the project. Please do contact me at the earliest if you find that you can work on it. Contact me if you have any questions and I can provide you with more information with regards to the project. I would like for you to communicate frequently with me about the project - even daily if possible. Please only take on the project if you can guarantee getting it done by the deadline specified.
In simple terms this is what the project is about:
1) Obtain the sequences for the pair described in Prosite from Swissport - I can get this part, and provide you with the sequences. Sp1 & Sp2 represent the two sets of sequences
2) Run all pairwise comparisions between the two sets to obtain set S = Sp1 U Sp2 using the program provided by Arvind Gopu (available in the given files).
3) On the web display a list of the sequences with check boxes and cut off values - Cblast, Chmm & Call - which will be dynamically chosen by the user.
4) Using the cut off value you obtain a seed set of sequences (from comparision - those that fit within the cutoff)
5) Use the seed set to perform BLASTpgp against the main set S. Bq is the set obtained from BLAST using the seed set, and Br is the set of the remaining sequences (from S)
6)Do the same with HMM. Build HMM model with the seed set using HMMbuild, and the run HMMsearch against the set S. to obtain Hq and Hr.
7) Present a visualization using the Graph packages to show Bq and Br and the connections between the different sequences. Do same for Hq and Hr and Sp1 and Sp2.
8) The basic goal is to see whether HMM is more sensitive than BLAST.
Let me know if you have any questions.
1) Complete and fully-functional working program(s) in executable form as well as complete source code of all work done.
2)Program should have plenty of comments, and written with good stlye.
3) Installation package that will install the software (in ready-to-run condition) on the platform(s) specified in this bid request.
4) Exclusive and complete copyrights to all work purchased. (No GPL, 3rd party components, etc. unless all copyright ramifications are explained AND AGREED TO by the buyer on the site).
Should be on a Unix Platform
Written in Perl and CGI. Check before using Perl modules other than [url removed, login to view] and BioPerl.
The programs should be written in PERL and CGI for a Unix platform. You may use [url removed, login to view], and BioPerl, and Set modules. If you plan on using other one please get in touch with me first as they may not be available on my machine, and the program will not work at my end.
Also the program requires use of tools that I can provide you access for you if you have trouble getting to them.