Good morning.
I am a student of department of Life Science, Handong Global University, South Korea.
I am taking a class named "Bioinformatics", and I am trying to mimic your paper,
"I-TASSER: a unified platform for automated protein structure and function prediction"
to be farmiliar with bioinformatics tools and concepts about sequence alignmnet, threading, protein, and so on.
To understand your paper deeply and enoughly, I am reading this paper step by step.
During studying it, I started to hope that mimic this paper also one by one.
Then I thought that I-TASSER is showing me a result page that was conducted through some series of other tools such as LOMETS, COACH, and etc, it also looks visit some databases such as PDB.
With this idea, I started to wonder how this I-TASSER conducted. How it goes to protein database, then conduct sequence alignment and threading, use those outputs as inputs for other tools, ...
What I want to know is how it works, where does it visit (does it visit your own database?), and what it uses.
Is it programmed to use some outputs for inputs? how my query sequences processed (do one of your team members implement for each sequences for us? or is it working automatically?)? or is there any programming language used (python, C++, R, etc..)?
Because as I told you before, I am hoping to mimic I-TASSER's result page without I-TASSER run. I want to use all other tool listed on left side of your lab's page.
Then which tools can I use and what to give as inputs for each programms?
I am just want to do this for my study and understanding this paper.
If you don't mind, would you tell me what can I do?
p.s_1
: I just submitted an sequence to I-TASSER and got message as below, then could you tell me some processes that this sequence will be treated with?
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The sequence has been successfully submitted to the I-TASSER server.
Your job id number is S434188. You will be notified by email once the job is completed if an email has been provided. The results of structure and function predictions for your submitted sequence will be available at (You may bookmark this link for your convenience of future visit): http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S434188/.
Your submitted sequence is of 14 residues:
>Q6AVM3_321-334
ARRKLRAAAIASVL
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p.s_2
: when I have a query sequence its length is under 10, what is the best way to use this?
I tried to add some repeated amino acid, for example, (sequence of length 4)+RRRRRR
or repeated the sequence, for example, SEQ_SEQ_SEQ_SEQ
are they good try? or can i improve my trial in that situation? is there any amino acid sequence that is good for add after short sequence?
if there is, would you suggest some candidates for me?
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Thank you for your help,
Sincerely,
Bugyeom_Im, 21100582,
School of Life Science
Handong Global University,
Pohang, GyeonSang buk-do,
South Korea.