To build SVM model for amino acid using composition of AA in r.
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@pujapatel5400-8292
Last seen 6.5 years ago
India

Give me the solution for my question composition of AA i found from the sequence of AA but i don't know how to classify the AA in r give me the suggestion and code.

svm r • 947 views
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@steve-lianoglou-2771
Last seen 2 hours ago
United States

It would be very helpful if you explain your problem a bit more clearly. As it stands now, it's hard to decipher what you mean.

That having been said, there are a few relatively new Bioconductor package that deal with kernel based analyses of biological sequences:

It would likely be very helpful for you to read through their vignettes to look at the types of analyses they enable and how to go about doing them.

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@pujapatel5400-8292
Last seen 6.5 years ago
India

Thank you for suggestion.

My question is i have one fasta file in that i have 6 different sequences from that sequences i found  composition of 20 amino acids, that values are in percentage. So i got one table of 20 AA's values and averages and then i want to build SVM model for that 20 AA's, but i don't know how to build and how to take positive and negative values for SVM. all the things i am try to built in R and MATLAb. 

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Have you read through the vignettes for those package to see what types of things you can do, and what type of data you need to do them?

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yes i read those pdf and tried to implement through those packages but it not worked.

>HMPREF9352_0001 CHAP domain protein [Streptococcus gallolyticus subsp. gallolyticus TX20005]
MKKRILSAVLVSGVTLGTAAATVNADDYDTQIAAQDAVISNLTSEQAAAQSQVDALQEQV
TSLQSQQDELEAQNAQLEAESQKLSEEIQALSSKIVARNESLKKQARSAQKTNTATSYIN
TILNSKSISDAINRVAAVREVVSANEKMLEQQEADKAAIEQKQAENQEAINTVAANKATI
EQNQAALATQQAELEAAQLNLSAQLATAEDEKASLVAQKEAAEQAAAEAAAAQAAAEAQA
QAEAEAQAASVAQAQESVENGTATVDTTTDTSSQDSTTASTDTAAATEDTSSTQQAATVT
PTATTTTSSSSSSSSASSSSSSSSSASTSSTASTSTSSSSSSSSSSSSVNTYPVGQCTWG
VKSLASWVGNNWGNANQWIASAQAAGHSVGTTPQVGAVAVWPYDGGGYGHVAYVTAVQSS
TSIQVMEANYAGNSSIGNYRGWFDPTSSTWGGGTVYYIYQ


I have that type of multiple sequences from that i found composition of each amino acids and i got numeric values then i want to apply SVM on AA classification.


seq1:18.91304 0.217391 3.478261 6.73913 0.217391 4.347826 0.434783 3.478261 3.26087 4.347826 0.652174 5 1.086957 9.782609 1.304348 15.86957 10.21739 6.73913 1.521739 2.391304
1seq2:.086957 0.217391 0.652174 0.652174 4.782609 1.521739 0.652174 4.347826 2.608696 7.173913 1.521739 1.304348 0.434783 0.652174 0.217391 2.826087 1.304348 2.391304 0 2.826087
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You haven't told us what you are trying to classify. All that we know is that you've got six amino acid sequences and you'd like to do "something" with them.

We don't know what that something is.

That having been said, you really can't do much of any type of supervised learning with just six observations (amino acid sequences, in your case).

You might try posting a new question that explains in a good amount of detail:

  • The biological problem you are exploring
  • The data you have collected in order to do so
  • Some approaches you might have tried already

Without those minimal pieces of information, there really isn't much anybody can do to help you, sorry.

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Yes it is bio logical problem how i can take classification or else prediction using SVM for amino acid, that's the big confusion in my mind. even i don't know how to do every thing.

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