FungalRV

FungalRV adhesin predictor software is developed in Perl and C. The standalone version can be downloaded and run on local system following the underlined instructions:

Click the link to download FungalRV adhesin predictor zipped file: FungalRV_adhesin_predictor.tar.gz

FungalRV adhesin predictor is distributed as a tar-gzipped file. It should be first unzipped and untarred by the command 'tar -xvzf FungalRV_adhesin_predictor.tar.gz' This will produce the following 13 items in the current directory.

• Model470a (Model file)
• Model470b (Model file)
• Model449c (Model file)
• Model26a (Model file)
• Model6c (Model file)
• calc_aafreq.c (C source code for calculating amino acid composition)
• calc_dipep_freq.c (C source code for calculating dipeptide frequencies)
• calc_tripep_freq.c (C source code for calculating tripeptide frequencies)
• calc_multiplets.c (C source code for calculating multiplet frequencies)
• calc_hdr_comp.c (C source code for calculating hydrophobic composition)
• run_fungalrv_adhesin_predictor.pl (The main Perl script for running the software)
• demo_file.txt (FASTA format sample input file)
• demo_result.txt (Sample output file generated by faap)
• binaries for ia32 bit machine

Other requirements:

The svm_classify is a part of the Joachim's SVM^light package. The source code of the package is available at Joachim's website .

Compile the SVM^light source code on your local machine that makes two executables, SVM_learn and SVM_classify. Copy the file SVM_classify and paste into the FungalRV_adhesin_predictor folder.

Also compile the C programs, calc_aafreq.c, calc_dipep_freq.c, calc_tripep_freq.c, calc_hdr_comp.c and calc_multiplet_freq.c and put the executables in the same folder. Now, the standalone version is ready to use.

For running FungalRV adhesin predictor, change to the FungalRV_adhesin_predictor directory and run the main Perl script run_fungalrv_adhesin_predictor.pl using the following command:   perl   run_fungalrv_adhesin_predictor.pl

If working on 32 bit machine, simply copy the binaries provided in the directory binaries for ia32 bit machine into the main FungalRV_adhesin_predictor directory and then run the perl script run_fungalrv_adhesin_predictor.pl

Export Data option is provided against all the data fetched by the user for both first and second layers. User has to tick the checkboxes corresponding to the data interested and then press the submit button. For second layer data can be fetched agaist one or more Orf Ids(Orf ID field is compulsary for second layer). In the result page Export Data option is provided. User can export the entire data fetched by clicking on Export Data link.