Question: Prediction of peptide function, How to do?
0
gravatar for Leite
2.6 years ago by
Leite410
Leite410 wrote:

Hello everyone,

I have several peptide sequences and I would like to know their function, is there any
software for this?

Thank you.

ADD COMMENTlink modified 2.6 years ago by Petr Ponomarenko2.6k • written 2.6 years ago by Leite410
1

use BLAST2GO, it will do it for you and very easy to use.

ADD REPLYlink written 2.6 years ago by ashish220

Thank so much for reply, Its a example:

Peptide FLDGTY FLDDTY FTFF DFPWPW WVLAW LEEGEWE WLAF DSEFL

ADD REPLYlink written 2.6 years ago by Leite410
1
gravatar for Petr Ponomarenko
2.6 years ago by
United States / Los Angeles / ALAPY.com
Petr Ponomarenko2.6k wrote:

It depends on your peptide length, organism you are studying and how deep into details you want to dive in. A good starting point is to run blastp https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins against NR or swissprot databases and see if the match maks sence.

ADD COMMENTlink written 2.6 years ago by Petr Ponomarenko2.6k

I've tried Blas2go and https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins But unsuccessfully.

ADD REPLYlink written 2.6 years ago by Leite410
1

I used your FLDGTY FLDDTY FTFF DFPWPW WVLAW LEEGEWE WLAF DSEFL in https://blast.ncbi.nlm.nih.gov/Blast.cgi and found no significant similarity to NR (All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects). It is not "unsuccessful" as you say, it just found no significant hits. Please tell us more about your peptides. Where do you get them? What are the species you are studying? Are these complete sequences or only parts?

ADD REPLYlink written 2.6 years ago by Petr Ponomarenko2.6k

Hey Petr Ponomarenko, Thank you so much for reply.

Where do you get them? Hydrolyzate of a plant seed with the alcalase enzyme. I did antioxidant activity test, it was positive. So I did mass spectrometry with this hydrolyzate and got those peptides.

Are these complete sequences or only parts? Example: FLDGTY this is a complete sequence.

So I would like to know which of these peptides is probably the holder antioxidade activity.

ADD REPLYlink written 2.6 years ago by Leite410

Oh, I thought that "FLDGTY FLDDTY FTFF DFPWPW WVLAW LEEGEWE WLAF DSEFL" is your peptide written that way with spaces for some reason. If these are 8 short peptides FLDGTY, FLDDTY, FTFF, DFPWPW, WVLAW, LEEGEWE, WLAF, DSEFL than I need to think a bit. Maybe BioStars community can help you now when we understand your task better. Thank you

ADD REPLYlink written 2.6 years ago by Petr Ponomarenko2.6k

Hello Petr Ponomarenko, Thank you for reply. And sorry for not explaining the doubt better. Yes it's a short peptides: FLDGTY, FLDDTY, FTFF, DFPWPW, WVLAW, LEEGEWE, WLAF and DSEFL

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Leite410
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1020 users visited in the last hour