Solid features to extract from protein sequences?
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5.0 years ago
unksci ▴ 160

I am looking for a solid set of features that can be extracted from protein sequences. Ideally these features capture different, and diverse aspects of the chemistry of the proteins. I do not care about the specific features, - but I would need features / predictions, which are quite accepted.

While I noted that some webpages list collections of various bioinformatic tools for that purpose (e.g.: http://www.expasy.org/proteomics ) , I was wondering, which tools experienced bioinformaticians would consider to be trustworthy, useful and solid for general-purpose comparison on metazoan proteomes (especially if different tools seem to serve the same purpose)

proteins features sequence • 917 views
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5.0 years ago
natasha.sernova ★ 3.8k

For example, see these sites:

http://www.ebi.ac.uk/Tools/pfa/

These tools below are for everything, find protein application in the middle:

http://molbiol-tools.ca/

You've asked for protein chemistry:

http://molbiol-tools.ca/Protein_Chemistry.htm

Human proteome and alternative splicing:

Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing

http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003030

Structural features. Old, but highly cited paper:

Structural Characterization of the Human Proteome

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC187559/

and see these papers for protein - DNA interactions:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475627/

Extracting sequence features to predict protein–DNA interactions: a comparative study

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149858/

Absence of a simple code: how transcription factors read the genome

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