These are some tools help you to find motifs and classification of protein families.

Interpro - https://www.ebi.ac.uk/interpro/

CDART- https://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi

Motifscan- https://myhits.isb-sib.ch/cgi-bin/motif_scan

few more servers:

Motif search_ https://www.genome.jp/tools/motif/

GimmeMotifs_ http://gimmemotifs.readthedocs.io/en/master/

SMART, PROSITE,

Scooby domain prediction- http://www.ibi.vu.nl/programs/scoobywww/

DIAL- http://caps.ncbs.res.in/DIAL/

PURE- http://caps.ncbs.res.in/PURE/PURE.html

PDBeMotif.

Hello all, thanks for answers,

I know most of these servers, the question was which one is currently the best for de novo motif search (i. e. for discovery of new motifs, previously unknown, but common to user defined set of sequences). Such tool is for example GLAM2 (http://meme-suite.org/tools/glam2) - "Perform motif discovery for gapped motifs on DNA or protein datasets". Does anyone know better tool/server for de novo motif discovery?

Thanks for opinions/reccomendations

Martin

Hi Martin,

Hope, I seen several article used MEME suit.

Did you tried this server from my earlier post.

Finding de novo motif using Python scripts.

GimmeMotifs_ http://gimmemotifs.readthedocs.io/en/master/

van Heeringen SJ and Veenstra GJC, GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments, Bioinformatics. 2011 Jan 15;27(2):270-1. doi: 10.1093/bioinformatics/btq636.

Even other software and servers has 5 star level in finding motifs search

Weeder_http://159.149.160.51/modtools/

HOMER_http://homer.ucsd.edu/homer/motif/

kmerHMM_http://www.cs.toronto.edu/~wkc/kmerHMM/index.html

BaMM web server for de-novo motif discovery and regulatory sequence analysis_https://bammmotif.mpibpc.mpg.de/

DMINDA2_http://bmbl.sdstate.edu/DMINDA2/

regards,

Rajesh

Thank you very much, Dr. Rajesh,

I will try, your tips look great.

Best regards

Martin