Use standalone version

Use fDOG with one seed sequence

fDOG will run smoothly with the provided sample input file infile.fa if everything is set correctly.

fdog.run --seqFile infile.fa --jobName test --refspec HUMAN@9606@3

The output files with the prefix test will be saved at your current working directory. You can have an overview about the available options with the command

fdog.run -h

The output consist of these text files (note: test is your defined -seqName parameter)

1. test.extended.fa: a multiple FASTA file containing ortholog sequences and the query gene
2. test.extended.profile: a tab-delimited file containing list of orthologous sequences and their correspoding similarity scores by comparing their feature architectures with the one of the query gene (for more info about this score, please read this document)
3. test.phyloprofile: an input file for visualisation the phylogenetic profile of the query gene using PhyloProfile tool
4. test_forward.domains and test_reverse.domains: a protein domain annotation file for all the sequences present in the orthologous group. The _forward or _reverse suffix indicates the direction of the feature architecture comparison, in which _forward means that the query gene is used as seed and it orthologs as target for the comparison, while _reverse is vice versa.

Use fDOG with multiple seed sequences

To run fDOG with multiple seed sequences, one can use fdogs.run function:

fdogs.run --seqFolder /seed/folder --jobName test --refspec HUMAN@9606@3

The only difference in the options of fdogs.run and fdog.run is instead of a single input sequence specified by --seqFile, fdogs.run takes a folder that contains multiple seed proteins as input that specified with --seqFolder, and the output files will be named based on the job name that is defined by --jobName. Other options as well as the output files are the same as fdog.run function.