OnWorks favicon

metastudent - Online in the Cloud

Run metastudent in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command metastudent that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



metastudent - predictor of gene ontology terms from protein sequence


metastudent -i FASTA_FILE -o RESULT_FILE_PREFIX [--debug] [--keep-temp] [--silent]
[--output-blast] [--blast-only] [--all-predictions] [--ontologies=MFO or BPO or CCO or
MFO,BPO or ...] [--with-images] [--blast-kickstart-databases=BLAST_RESULT_FILE(S)]
[--temp-dir=DIR] [--config=CONFIG_FILE] !!! Make sure your fasta file contains at most 500
sequences !!!


Metastudent predicts Gene Ontology (GO) terms from the Molecular Function Ontology (MFO),
Biological Process Ontology (BPO) and Cellular Component Ontology (CCO) for input protein
sequences by homology-based inference from already annotated proteins.

Large (1 GB in total) data files necessary for the operation of metastudent are downloaded
automatically on the first use of the program. The download is restartable. You can also
make an explicit call to
metastudentdata (by default /usr/bin/metastudentdata) to download the data files.
In case the data directory (by default /usr/share/metastudent-data) is not writable and
you are not root, the operation is
reattempted with sudo(8).

Output format
For each selected ontology (see --ontologies), one output file is produced (see -o). Each
line in each file associates a protein with a GO term and a reliability for the
association (0.0 to 1.0). The following format is used: <PROTEIN


Hamp, T., Kassner, R., Seemayer, S., Vicedo, E., Schaefer, C., Achten, D., ... & Rost, B.
(2013). Homology-based inference sets the bar high for protein function prediction. BMC
Bioinformatics, 14(Suppl 3), S7.


The input fasta file. Please try to remove any special formattings (e.g. whitespaces)
in the sequences before using them as input. Due to high memory usage, make sure your
fasta file contains at most 500 sequences.

The file name prefix of the output files. GO terms are organized in ontologies.
Metatstudent treats each ontology differently and outputs one result file for each.
For example, if <RESULT_FILE>=./myresult and MFO (Molecular Function Ontology) and BPO
(Biological Process Ontology) ontologies are selected (see option --ontologies), then
metastudent creates two output files: ./myresult.MFO.txt and ./myresult.BPO.txt.

Print extra debugging messages.

Whether to keep the temp directories after metastudent has finished (they can be
useful when errors occur or in combination with --blast-kickstart-databases).

No progress messages (stdout), only errors (stderr).

Whether to output the result of the BLAST runs. Useful in combination with
--blast-kickstart-databases. Output file name format is

Whether to only output the result of the BLAST runs, and nothing else. See options
--output-blast and --blast-kickstart-databases.

Whether to output the prediction results of the individual predictors. File name
format of the output file is <RESULT_FILE_PREFIX>.<ONTOLOGY>.<METHOD>.txt.

Whether to exclude the actual GO term names as a column in the output prediction

Whether to also generate an image that displays the predicted GO terms as a GO graph.
This option can only be used with exactly one input sequence and only when connected
to the internet.

--ontologies=MFO or BPO or CCO or MFO,BPO or ...
A comma separated list of ontologies to create predictions for. Default is
MFO,BPO,CCO. If used in combination with --blast-kickstart-databases, the number and
order of the ontologies must correspond to the kickstart files.

Since running BLAST is usually the part that takes the longest in metastudent, this
option allows you to re-use the output of a previous run. This is useful to test, for
example, different parameters or when you have lost a prediction. The number of
kickstart files must correspond to the number of ontologies (see option --ontologies).
Separate the file paths with commas. For example:
--blast-kickstart-databases=<RESULT_FILE_MFO>,<RESULT_FILE_BPO> (kickstart for both
ontologies) or --blast-kickstart-databases=,<RESULT_FILE_BPO> (only kickstart BPO;
note the comma).

The parent temp directory to use instead of the one specified with tmpDir in the
metastudent configuration file.

The path to a custom metastudent configuration file; overrides all settings of the
configuration files found in the FILES section of this man page.

Use metastudent online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    TurkDevOps a�?k kaynak yaz?l?m
    geli?tirici topluluklar? DevTurks-Team
    Taraf?ndan desteklenmektedir..
    Download turkdevops
  • 2
    *asammdf* is a fast Python parser and
    editor for ASAM (Associtation for
    Standardisation of Automation and
    Measuring Systems) MDF / MF4
    (Measurement Data Format...
    Download asammdf
  • 3
    LAME (Lame Aint an MP3 Encoder)
    LAME (Lame Aint an MP3 Encoder)
    LAME is an educational tool to be used
    for learning about MP3 encoding. The
    goal of the LAME project is to improve
    the psycho acoustics, quality and speed
    of MP...
    Download LAME (Lame Aint an MP3 Encoder)
  • 4
    A set of Python extension modules that
    wrap the cross-platform GUI classes from
    wxWidgets.. Audience: Developers. User
    interface: X Window System (X11), Win32 ...
    Download wxPython
  • 5
    This is the Total War pack file manager
    project, starting from version 1.7. A
    short introduction into Warscape
    modding: ...
    Download packfilemanager
  • 6
    A network traffic tool for measuring
    TCP and UDP performance with metrics
    around both throughput and latency. The
    goals include maintaining an active
    iperf cod...
    Download IPerf2
  • More »

Linux commands