How Can I Upload Pssm In Blast Tool?
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10.3 years ago

Hello,

My research area is Data mining and my work on that is regarding "Protein Secondary Structure Prediction using support vector machine". I’m using CB513 &RS126 dataset.I run the sequence without using PSI-BLAST. But I got wrong result because of insufficient features and then I have read many papers regarding the sufficient and insufficient feature. I understand that, we have to run the sequence in PSI- BLAST for much iteration and see for which sequence we get high accuracy and use that particular sequence for structure prediction, is it right? I thought to confirm what I have understand. The output from the BLAST is completely different from the input I gave, Next doubt is we are giving only amino acid sequence (primary sequence), how we can get secondary structure for result in sequence. How to view the PSSM from PSI-BLAST. What is scoremat? why do we need to BLAST the amino acid sequence? In Basic Local Alignment Search Tool,how to upload PSSM? My research is right or wrong. Please tell me the correct way. How can I precede my research work?

Please kindly reply I have less time to complete my research work

pssm feature • 2.2k views
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It's unlikely that anyone will even try to answer this question. Let me give you some advice. First, don't be so formal. You're not writing to a professor for a job; this is a community of people, including many "madams". Second, you asked about a dozen separate questions at once. You need to define clearly what your problem is, what you have tried and why you are unable to proceed. Third, it sounds like your project is part of a university course (Masters?) We are not really the appropriate people to advise you. Surely you have advisers or peers closer to the project who can help you.

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By the way, there is an "edit" button next to your question. You can improve your question a bit by using it (instead of posting a new one).

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