SLiMFinder Help Pages

Original SLiMFinder publication

When using SLiMFinder results in a publication, please cite the main PLoS One paper:

• Edwards RJ, Davey NE & Shields DC (2007): SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE 2(10): e967. [PLoS One.] [PubMed]

In addition, SLiMFinder uses the following underlying software:

• Altschul SF, Gish W, Miller W, Myers EW & Lipman DJ (1990): Basic local alignment search tool.
  J. Mol. Biol. 215:403-410.

Disorder prediction

If using IUPRED disorder prediction to mask input sequences and/or filter results, please cite:

• Dosztanyi Z, Csizmok V, Tompa P & Simon I (2005): IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21:3433-3434.

GOPHER orthologues and conservation masking

If using Relative Local Conservation masking, in addition to the GOPHER citations (below) and IUPRED disorder predictions, please cite:

• Davey NE, Shields DC & Edwards RJ (2009): Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics 25(4): 443-50. [Bioinformatics.] [PubMed]

If using alignments of homologous proteins, generated by GOPHER, please cite:

• Davey NE*, Edwards RJ*, Shields DC (2007): The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res. 35(Web Server issue):W455-9. [Nucleic Acids Res.] [PubMed]
  *Joint first authors
• Edgar RC (2004): MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
  BMC Bioinformatics 5:113.

Advanced SLiMChance Statistics

If using the SigV advanced SLiMChance statistics,please cite:

• Davey NE, Edwards RJ & Shields DC (2010): Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. BMC Bioinformatics 11: 14. [BMC Bioinformatics.]