Problem with SLiMFinder bioware webserver

There is currently a problem with the SLiMFinder webserver hosted at UCD, where masking is failing to be performed, regardless of settings. This severely impacts the quality of results. (Disorder, low complexity and n-terminal methionine masking are generally recommended for SLiMFinder.)

I am in communication with the Shields lab to try and get the issue fixed but, until it has been rectified, the bioware.ucd.ie SLiMFinder webserver should not be used.

If you wish to run SLiMFinder online, you can do so via the SLiMFinder REST server (see BioInfoSummer 2016 workshop), which can also be run from within Cytoscape using the SLiMScape App.

Sequence names and species codes for GOPHER

GOPHER (and any tools using orthologue alignments produced by GOPHER) needs sequence names to be formatted in a particular way so that the species information can be corrected parsed. This “SLiMSuite fasta” format is the only sequence format fully supported by SLiMSuite. If you are getting an unexpected error, sequence formatting and naming is one of the first things to check. It should not break any other programs that I know about.

This format is:

>Gene_SPCODE__AccNum [Description]
SEQUENCE

Where:

• Gene is not used for anything and is purely for easy visual identification.
• SPCODE is the species code. Where possible, Uniprot species mnemonics should be used but any short code can be used as long as (a) it contains uppercase letter and numbers only (no symbols), and (b) it is consistently used within a species/database. (i.e. you can make it up as long as all sequences from the same species use the same code.)
• AccNum is the accession number, which is what is used as the unique sequence identifier.
• Description is optional and can contain any other text.
• SEQUENCE can be on one or more lines and contain spaces. However, it is best to have a single SEQUENCE line with no whitespace. (Some programs may enforce this.)

Seqsuite can be used to rename and reformat sequences, using the seq and seqlist programs.

Uniprot downloads should be automatically recognised and converted where needed.

How to Cite SLiMSuite programs

Most programs in the SLiMSuite package have citation instructions in their docstring. Either run with the help or help option (or if running through SLiMSuite or SeqSuite, use help=T) to bring up that information. Alternatively, the online documentation should show the papers to cite.

You can retrieve documentation for a given program by replacing slimsuite in the box below and clicking View Documentation.

for:

If a program does not have its own citation, please cite SLiMSuite using: Edwards RJ & Palopoli N (2015): Computational Prediction of Short Linear Motifs from Protein Sequences. Methods Mol Biol. 1268:89-141.

For general use or reuse of code, please cite the Zenodo DOI for the GitHub release:

External programs

See External Components of SLiMSuite for citing programs that SLiMSuite uses.

Log Files

Every program generates a log file when it is run. By default, this file will be named after the calling program (e.g. gasp.py will produce a log called gasp.log) but this can be changed with the log=FILE option. The basefile=X option will also set the base name of the log file, as well as the main results files (for most programs). Logs will be appended unless the newlog (or newlog=T) option is used.

The log file records information that may help subsequent interpretation of results or identify problems. Each line is tab delimited in the form:

#XXX    HH:MM:SS    Log Message.

Where #XXX is an identifier that can be used to parse out specific types of information, HH:MM:SS is the runtime in hours, minutes and seconds, and Log Message will be something (hopefully) informative.

All log files start with the same few lines:

#~~#    #~~#    #~~#
#LOG    00:00:00    Activity Log for PROGRAM X.X: DATE TIME YEAR
#DIR    00:00:00    Run from directory: RUNPATH
#ARG    00:00:00    Commandline arguments: ARGLIST
#CMD    00:00:00    Full Command List: [FULL ARGLIST]

This should contain all the information required to repeat the analysis:

• PROGRAM X.X: DATE TIME YEAR will have the program name, version number and the date/time of the run.
• RUNPATH is the directory from which the program was run.
• ARGLIST is the list of command-line arguments given to the program.
• FULL ARGLIST is the full list of command-line arguments including any arguments read in from ini files.

The last line can help identify the source of any unexpected behaviour due to default settings etc.

(The #~~# #~~# #~~# line is simply to act as a separator if appending an existing log file.)

If the program runs to completion successfully, it will end with another #LOG line:

#LOG    HH:MM:SS    PROGRAM V:X.X End: DATE TIME YEAR

If this line is not present then something went wrong during the run (see Error Messages, below - or it is still in progress. Other information is also recorded along with the runtime (HH:MM:SS since the program started). For help interpreting log files, please check the relevant software manual or contact me if the information is missing. (Hopefully, the log content is mostly self-explanatory but I shall add any explanations I have to send people to the relevant manual’s appendix.)

Error Messages

One of the most important aspects of the log file is to register any error messages. These are marked by an #ERR line header. Hopefully, there will not be any but if there was a problem with the run then these lines should contain the details. To catch these lines separately, errorlog=FILE will output error messages to an additional file.