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

    Input

    RefSeq Protein ID
    Enter the Identifier of the query. Only RefSeq Identifiers from the NCBI RefSeq protein database are valid (example: NP_595754).

    Search Options

    Database
    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.

    E-value
    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.

    Low-Complexity Filtering
    Turn filtering of low-complexity regions in proteins on or off. Default: on.

    Composition-based Statistics
    Method to adjust the matrix to compensate for amino acid composition. See more information on composition-based statistics @ the NCBI.

    Job Options

    E-mail (optional)
    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]

    Options:
    -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