Program: SLiMSearch Description: Short Linear Motif Search tool Version: 1.7.1 Last Edit: 03/12/15 Citation: Davey, Haslam, Shields & Edwards (2010), Lecture Notes in Bioinformatics 6282: 50-61.

Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_seq rje_sequence rje_scoring rje_slim rje_slimcore rje_slimcalc rje_slimlist rje_zen

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

SLiMSearch is a tool for finding pre-defined SLiMs (Short Linear Motifs) in a protein sequence database. SLiMSearch can make use of corrections for evolutionary relationships and a variation of the SLiMChance alogrithm from SLiMFinder to assess motifs for statistical over- and under-representation. SLiMSearch is a replacement for PRESTO and uses many of the same underlying modules.

Benefits of SLiMSearch that make it more useful than a lot of existing tools include:

• searching with mismatches rather than restricting hits to perfect matches.
• optional equivalency files for searching with specific allowed mismatched (e.g. charge conservation)
• generation or reading of alignment files from which to calculate conservation statistics for motif occurrences.
• additional statistics, including protein disorder, surface accessibility and hydrophobicity predictions
• recognition of "n of m" motif elements in the form <X:n:m>, where X is one or more amino acids that must occur n+
times across which m positions. E.g. <IL:3:5> must have 3+ Is and/or Ls in a 5aa stretch.

Main output for SLiMSearch is a delimited file of motif/peptide occurrences but the motifaln=T and proteinaln=T also allow output of alignments of motifs and their occurrences. The primary outputs are named *.csv for the occurrence data and *.summary.csv for the summary data for each motif/dataset pair.

NOTE: SLiMSearch has now been largely superseded by SLiMProb for motif statistics.

Commandline

### Basic Input/Output Options ###
motifs=FILE : File of input motifs/peptides [None]
Single line per motif format = 'Name Sequence #Comments' (Comments are optional and ignored)
Alternative formats include fasta, SLiMDisc output and raw motif lists.
seqin=FILE : Sequence file to search [None]
batch=LIST : List of sequence files for batch input (wildcard * permitted) []
maxseq=X : Maximum number of sequences to process [0]
maxsize=X : Maximum dataset size to process in AA (or NT) [100,000]
maxocc=X : Filter out Motifs with more than maximum number of occurrences [0]
walltime=X : Time in hours before program will abort search and exit [1.0]
resfile=FILE : Main SLiMSearch results table [slimsearch.csv]
resdir=PATH : Redirect individual output files to specified directory (and look for intermediates) [SLiMSearch/]
buildpath=PATH : Alternative path to look for existing intermediate files [SLiMSearch/]
force=T/F : Force re-running of BLAST, UPC generation and search [False]
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SearchDB Options I

masking=T/F : Master control switch to turn off all masking if False [False]
dismask=T/F : Whether to mask ordered regions (see rje_disorder for options) [False]
consmask=T/F : Whether to use relative conservation masking [False]
ftmask=LIST : UniProt features to mask out [EM,DOMAIN,TRANSMEM]
imask=LIST : UniProt features to inversely ("inclusively") mask. (Seqs MUST have 1+ features) []
compmask=X,Y : Mask low complexity regions (same AA in X+ of Y consecutive aas) [5,8]
casemask=X : Mask Upper or Lower case [None]
motifmask=X : List (or file) of motifs to mask from input sequences []
metmask=T/F : Masks the N-terminal M [False]
posmask=LIST : Masks list of position-specific aas, where list = pos1:aas,pos2:aas [2:A]
aamask=LIST : Masks list of AAs from all sequences (reduces alphabet) []

SearchDB Options II

efilter=T/F : Whether to use evolutionary filter [False]
blastf=T/F : Use BLAST Complexity filter when determining relationships [True]
blaste=X : BLAST e-value threshold for determining relationships [1e=4]
altdis=FILE : Alternative all by all distance matrix for relationships [None]
gablamdis=FILE : Alternative GABLAM results file [None] (!!!Experimental feature!!!)
occupc=T/F : Whether to output the UPC ID number in the occurrence output file [False]
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### SLiMChance Options ###
maskfreq=T/F : Whether to use masked AA Frequencies (True), or (False) mask after frequency calculations [True]
aafreq=FILE : Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) [None]
aadimerfreq=FILE: Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) [None]
negatives=FILE : Multiply raw probabilities by under-representation in FILE [None]
background=FILE : Use observed support in background file for over-representation calculations [None]
smearfreq=T/F : Whether to "smear" AA frequencies across UPC rather than keep separate AAFreqs [False]
seqocc=X : Restrict to sequences with X+ occurrences (adjust for high frequency SLiMs) [1]
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### Output Options ###
extras=X : Whether to generate additional output files (alignments etc.) [1]
- 0 = No output beyond main results file
- 1 = Generate additional outputs (alignments etc.)
pickle=T/F : Whether to save/use pickles [True]
targz=T/F : Whether to tar and zip dataset result files (UNIX only) [False]
savespace=0 : Delete "unneccessary" files following run (best used with targz): [0]
- 0 = Delete no files
- 1 = Delete all bar *.upc and *.pickle files
- 2 = Delete all dataset-specific files including *.upc and *.pickle (not *.tar.gz)

• See also rje_slimcalc options for occurrence-based calculations and filtering *
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History Module Version History

    # 0.0 - Initial Compilation.
    # 1.0 - Standardised masking options. Still not fully tested.
    # 1.1 - Added background=FILE option for determing mean(p1+) for SLiMs based on background file.
    # 1.2 - Added maxsize option.
    # 1.3 - Add aamask option (and alphabet)
    # 1.4 - Fixed zero-size UPC bug.
    # 1.5 - Add MaxOcc setting.
    # 1.6 - Minor tweaks to Log output. Add option for UPC number in occ output.
    # 1.7 - Modified to work with GOPHER V3.0.
    # 1.7.1 - Minor modification to docstring. Preparation for update to SLiMSearch 2.0 optimised for proteome searches.