PUFAS is a web server that predicts the possible function of an input sequence obtained from next generation sequencing data. Function could be assigned on the basis of the predicted domains and fold. It uses a series of methods, including homology search, prediction of gene, secondary structure, domains, and fold, to assigned possible function of the proteins unknown function (PUFs). It allows an annotation of PUFs.
The analysis steps are as follows:

  1. Annotating PUFs with a FASTA format file, containing the assembled sequence generated using next generation sequencing platforms. The assembled sequence used for detecting function using BLAST (Nucleic Acids Res. 1997 Sep 1;25 (17):3389-402) programme against NCBI-nr database. Based on the homology it predicts the function. The user can select cutoff E- values and provide email id. The job is submitted by clicking the Annotate button. After submission of the job the user can see a page displaying the status of the job, and once the job is completed then the results will be shown on the same page. However, if user chooses to provide email, a link to the results page will be sent to that email upon completion of the job.

  2. The PUFs sequence was used for gene prediction using gene prediction tool i.e. Augustus (doi: 10.1093/nar/gkh379). It predicts the gene and provide the sequence. The protein sequence were used for further analysis.

  3. Protein sequence is used as input for annotating PUFs using NCBI CDD (doi: 10.1093/nar/gkq1189) and pfam (http://nar.oxfordjournals.org/content/42/D1/D222.long) as a sequence based method. It will show the possible predicted domains and its function.

  4. Protein sequence is used for annotating PUFs using GenThreader a fold prediction tool (J Mol Biol. 1999 Apr 9;287(4):797-815) is performed as a structure-based method.

  5. In a final step, the results can be downloaded and provided in the csv format. Users can download the output and they can filter the results based on the significance threshold values.


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