SLiM generator from aligned peptide sequences
Copyright © 2014 Richard J. Edwards - See source code for GNU License Notice
See SLiMSuite Blog for further documentation. See
This program has a fairly simple function of reading in a set of sequences and generating a regular expression motif
from them. It is designed with protein sequences in mind but should work for DNA sequences too. Input sequences can
be in fasta format or just plain text (with no sequence headers) and should be aligned already. If
SLiMMaker considers each column of the input in turn and compresses it into a regular expression element according to
some simple rules, screening out rare amino acids and converting particularly degenerate positions into wildcards.
Each amino acid in the column that occurs at least X times (as defined by
By default, each defined position in a motif will contain amino acids that (a) occur in at least three sequences
each, (b) have a combined frequency of >=75%, and (c) have 5 or fewer different amino acids (that occur in 3+
sequences). The same
Note. Unless the "iterate" function is used, the final motif only contains defined positions that match a given frequency of the input (75% by default). Because positions are considered independently, however, the final motif might occur in fewer than 75% of the input sequences. SLiMSearch can be used to check the occurrence stats.
Version 1.5.0 incorporates a new peptide alignment mode to deal with unaligned peptides. This is controlled by the
Version 1.6.0 added the option to incorporate amino acid equivalencies to extend motif sites beyond the top X% of
amino acids. This works by identifying a degenerate set of amino acids as normal using
If two or more equivalence groups could be extended, the one with the most members will be chosen. If tied, the one
with fewest possible amino acids (from
See also rje.py generic commandline options.
History Module Version History
# 0.0 - Initial Compilation. # 1.0 - Initial Working Version. Some minor modifications for SLiMBench including iterative SLiMMaker. # 1.1 - Modified to work with end of line characters. # 1.2.0 - Modified to work with REST servers. # 1.3.0 - Added varlength option to identify gaps in aligned peptides and generate variable length motif. # 1.3.1 - Fixed varlength option to work with end of peptide gaps. (Gaps ignored completely - should not be there!) # 1.4.0 - Add iteration REST output. # 1.4.1 - Add unmatched peptides REST output. # 1.4.2 - Fixed bug with variable length wildcards at start of sequence. # 1.5.0 - Added peptalign=X functionality, using PeptCluster peptide alignment. # 1.6.0 - Added equiv=LIST : List (or file) of TEIRESIAS-style ambiguities to use [AGS,ILMVF,FYW,FYH,KRH,DE,ST] # 1.6.1 - Fixed peptide case bug. # 1.7.0 - Added maxlen parameter.
SLiMMaker REST Output formats
Running SLiMMakerRun with
for more user-friendly formatted output. Individual outputs can be identified/parsed using
Available REST Outputs
Enter sequences and click "Make SLiM". Sequences can be raw sequences or fasta format.
(Example sequences are LIG_PCNA_PIPBox_1 ELM occurrences.)
In place of peptides, an ELM Class can also be entered into the box. See the REST aliases page for more details.
© 2015 RJ Edwards. Contact: email@example.com.