Welcome to the Help & Information pages of morFeus. Here, you will find information on using the web-server, interpreting the output, as well as on how to download the virtual machine of morFeus for local command-line usage.
morFeus web-server help
RefSeq Protein ID
Enter the Identifier of the query. Only RefSeq Identifiers from the NCBI RefSeq protein database are valid (example: NP_595754).
Chose the database you want to search against. You can chose between all species, eukaryota, fungi/metazoa, viridiplantae or bacteria. All database search options are based on the NCBI RefSeq protein database.
Chose the E-value cut-off for the BLAST and back-BLAST searches. Depending on your search query, you will chose either a low or high cut-off. For search queries with only remote similarity to orthologs, an initial setting of 100 is recommended.
Turn filtering of low-complexity regions in proteins on or off. Default: on.
Method to adjust the matrix to compensate for amino acid composition. See more information on composition-based statistics @ the NCBI.
You can enter your e-mail address for notification of finished jobs. The link to the morFeus results will be sent to you. Highly recommended, as morFeus jobs can take a long time (several hours).
morFeus command line options
You will have to download the morFeus virtual machine in order to use the command line options.
Summary of Command-line Options and a Short Description of their Function
Usage: morfeusd.py [options] id1 [id2 .. idn]
-h, --help show this help message and exit
-c, --cleanup (C)leanup morfeusd queue - required to clean up queue after failed job
-e EVALUE, --e-value=EVALUE (E)-value - chose the E-value for BLAST and back-BLAST jobs
-f, --file Input id (F)ile - chose Input (query); either use NCBI RefSeq ID or provide FASTA-formatted file
-g, --graph Draw network (G)raph - show network graph as output
-l, --local Use local BLAST queue - use local (as opposed to remote NCBI) BLAST queue; default: remote
-r, --re-run (R)u-run existing job - rerun a job; useful, as it saves time for back-BLASTing; enter job-ID after -r
-s, --skip (S)kip clustering (re-run) - skip the clustering step; can be used only with -r (re-run)
-n, --no-clustering (N)o clustering) - skip clustering step in new job; prevents clustering hits based on similarity of alignment and starts with back-BLASTs based on E-value