I have a set of ~40-50 protein sequences. I want to find motifs like MEME tool but most importantly, I want a tool that can extract a consensus sequence like a scanprosite pattern e.g. D-X-[KR]-P-{WYF}-X5.
I can do it manually but its a tedious job. Is there any free online tool that can extract such a pattern from a set of protein sequences? MEME output only include a consensus sequence and a logo.
Unsure of what currently exists but I could probably write something to do so. Sounds to me like it's just a bit of regex.
Check Consensus maker (link below)
Depending on what do you want to do afterwards, maybe creating a hmm profile would also be an alternative.
https://www.hiv.lanl.gov/content/sequence/CONSENSUS/consensus.html
Dear
I recommend you to check the following links.
Thank
https://molbiol-tools.ca/Motifs.htm
http://www.genome.jp/tools/motif/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC150457/
https://www.expasy.org/proteomics/families__patterns_and_profiles
https://www.expasy.org/resources/search/keywords:protein%20domain
If you're looking for specific motifs such as the example you provided, I recommend using unix common line functions (e.g. grep) with regex pattern matching. Assuming that the X5 at the end means that you want the match to end in a run of five copies of the same amino acid , with all possibilities allowed, the following will do what you need:
grep 'D.K\|RPW\|Y\|F.\(.\)\1\{4\}' sequence_filename -B 1
Essentially, the command queries the file named "sequence_filename" and looks for (i.e. greps): D followed by any amino acid, followed by K or R, followed by P, followed by W, Y or F, followed by any amino acid, followed a run of five instances of the same (but unspecified) amino acid. It then returns the matching line and a single line beforehand (-B 1)
Actually the pattern i gave is just an example. It could be any thing. After lots of search I found one called GLAM2. However, its pattern consisted of top two most common amino acids within that column and ignored others. The logo file it generates is fine but I am unable to read the less common amino acids which are squiished. Also I do not know how to run tools with command lines.
I am told SPLASH is good for this purpose.
HI there;
I have done LC-MS/MS for the tick salivary gland. Now the problem is that full genome sequence of Ixodidae is not available and when I am running it through some of the well known databases such as PANTHER, DAVID, ExPasy etc. it can only hit 10 to 12 sequences while the rest left as such. So is there anybody who can suggest me a free available software/database for proteomic analysis?
I know this is quite an old question but as I was looking for the same thing and found this thread. The best tool I could find for a predefined motif is: PATTINPROT https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_pattinprot.html
You can paste your protein and your motif and decide how stringent the cut-off for identifying a motif. Good luck.
- Badges
- Science topic
- Similar topics
- Phytochemistry
- Extracts