Types Of Bioinformatics Analysis To Perform On A Given Sequence
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12.7 years ago
Ssh3 ▴ 60

Hi, I am new to Bioinformatics. I was given a sequence of a protein (no 3D structure available) to perform bioinformatics analysis on it. What are the types of bioinformatics analysis can I carry out and what are the possible tools to perform the analysis on it? Thank you in advance! :)

sequence • 7.5k views
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What are you trying to find out about the protein? Without at least telling that, no one here will be able to help you.

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I think before getting harsh on someone it's better to ask them to revise question and get to the point. Beginning is difficult.

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12.7 years ago
Michael 54k

Let me first mention the following: imho, the reason why your question gets voted down, is that it displays an 'odd' type of motivation or lack thereof. Your primary goal seems to be a kind of 'somebody gave me that assignment which I don't fully understand, to apply an arbitrary tool, etc.', that's not how you are likely to arrive at a good solution and understanding. On the other hand, I understand that this can happen during your studies especially for a beginner, and that it is hard to get an entry point, when the motivation is (possibly, or not understood by the student) not provided by the teacher.

What you are asking here is sort of the initial question in bioinformatics (and thus it has been posed often, also on BioStar), so I would like to point to something to help you get the motivation and context:

In the end, your supervisor was possibly trying to point you at (and is now upset cause I help cheating ;) ):

  • BLAST against NR, Swissprot
  • InterPro Scan
  • PFAM

If you can use learn about these tools and how they work, apply them and understand the output, it will possibly help you most.

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12.7 years ago

I know this question is going to state the obvious, but I am going to write it anyway.

Bioinformatics is not about running software or doing analyses--at least not completely about those. The first step in an experiment (computational or otherwise and sometimes implied) is to define one or more relevant biologic questions. Particularly for someone coming from a more computational background with little biological expertise, this step can be challenging, but it is all-the-more-necessary if one brings little biological insight to the table.

So, in your situation, I would go back to the person who gave you the sequence and start asking questions. When you are done asking questions, go off and do some reading--and then go back to ask more questions. When you get a good idea of what your collaborator needs to know, it will be much easier to ask questions of others (even if the "others" include google!). As one gains experience, the translation from a biological experiment to an analytical framework for dealing with the data becomes easier.

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12.7 years ago
Thaman ★ 3.3k

If you are not to the point then you are never going to get answer as you have realized. But, this is a lesson. Be precise and do some question and answer to yourself instead of being random.

Some of Bioinformatics analysis you can do on Protein Sequence. Please go through individual links and learn about the tools. These are just a few.

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12.7 years ago
Bach ▴ 550

Astonishingly enough, the following search comes back with a ton of links which cover a couple of different aspects and where you should have a first look at to inform yourself: http://www.google.com/search?q=bioinformatics+protein+analysis

Apart from that, I'll second Lars by saying that you should get a bit more specific.

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He is not 'condescending', BaCh is rightfully pointing elfw to the fact that he could have achieved more for his/her own good by

  1. searching for an answer himself
  2. mentioning what he/she tried before
  3. being more specific about the biological question or the intentions of the 'supervisor'.
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What is hostile about pointing at problems and deficiencies with how a question is posed, and the motivation behind it? I agree, it is normally not optimal to give a google search as an answer, in this case it is a totally viable way to go.

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No need to get condescending...

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I agree with Michael and BaCh. It still amazes me how many people don't seem to try Google first to get an answer to their question (whatever that question may be ....).

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Great guys, excellent way to create a hostile and unwelcoming community. I refer to the FAQ: stackoverflow.com/faq#etiquette

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Martijn is not too far away from the truth. Though I would not call it "condescending", it's more "rather irritated."

I like helping people whatever their problem is (and in the process invest my time as others did in the past for me), but the display of complete unwillingness of some people to first do own basic research amazed me in 'ye olde Usenet times' and still continues to do so today on stackexchange and other boards on the internet.

If I had wanted to be mean and condescending, I would have used "Let Me Google That For You": http://lmgtfy.com/?q=bioinformatics+protein+analysis

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This looks pretty much like a split vote about netiquette for me, now let's focus on answering question again ;)

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If you guys have a problem with this question then simply do not answer/comment it !

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Great guys, excellent way to create a hostile and unwelcoming community. I refer to the FAQ: http://stackoverflow.com/faq#etiquette

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11.5 years ago
Paul ▴ 20

I would recommend:

www.expasy.org/tools/

Here you find numerous tools to check/predict secondary structure, helical wheel plot etc.

Furthermore it depends indeed as stated above on what you want. For example an idea of the topology of a membrane protein can be addressed by several approaches like:

TOPCONS TOPDB

You want an idea whether the protein is able to bind to lipids:

Heliquest

For other tips I refer to above answers.

Good luck!

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