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16

Well you are assuming one sequenced genome/proteome per NCBI tax id. That is no longer true. So if you click on the proteome filter it decreases by half. Which gets you into the 60,000 range. Now not all of these are "different" conceptual proteins, many are artifacts from the way GenBank/EMBL/DDBJ interact with the TrEMBL section of UniProtKB i.e. they are ...


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It sounds like you have considered most of the obvious alternatives (and thank you for clarifying the question). I suppose the first question in an alternatively spliced transcript with a retained intron is whether the open reading frame of the protein is maintained. If there is a termination codon that now becomes in-frame due to the intron then the ...


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Given your background (not a biologist or chemist) you would probably find the introductory material in a biochemistry "lite" textbook more accessible/useful than a hardcore text for specialists. As a co-author of a biochemistry textbook, I can tell you that there are essentially three different classes, or types of texts. Comprehensive textbooks, of ...


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This has been studied by some of my labmates in Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? I am not involved in their research, but here is the gist of the paper: Different scales are, as you say, developed based on different criteria. In particular, Eisenberg scale is one of the consensus ...


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There are 20+ thousand genes in the genome, but each of these can produce multiple proteins. In addition to this, you have protein fragments and cleavage products further increasing the number of entries.


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Don't be discouraged. At least in vitro, if there is ample chemical substrates (e.g. ATP) and protein A (i.e. kinase) remains active, the kinase will just keep phosphorylating its protein substrates (B alone or a mixture of B, C, D) until the substrates are depleted. Thus, all substrates will be phosphorylated eventually. The contrived Condition 1 may occur ...


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Some suggestions. For identifying function do a homology search. There is little functional annotation of lncRNAs. So homology based information can be obtained only for protein sequences. So you can try these: Check the coding potential. Find ORFs (perhaps set a minimum length cutoff). To be stringent you can also check for Kozak consensus sequences (for ...


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Interactions denote protein-protein interactions, which means physical association between proteins. By nature, these networks/graphs are undirected. Replication interactions (actually a not very good term) denote gene regulatory interactions that affect HIV replication. These sets also include the regulatory effects of HIV genes on host genes (and hence ...


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I want to add a book to the list that may be easier for you since it takes it from the perspective of Physics: Finkelstein & Ptitsyn, Protein Physics, Academic Press (2002). ISBN 0-12-256781-1. It covers structure, thermodynamical processes in proteins, mechanism of folding, function, a bit of bioinformatics. It is designed as a master level course in ...


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Sometimes SwissProt annotations come from direct experimental evidence, but this is rare. It depends on the entry, but more often than not the annotation will have been obtained by some kind of sequence analysis or prediction based on sequence similarity.


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Nanodiscs are very powerful technology for membrane protein invented in Stephen Sligar's lab at the University of Illinois. A nanodisc is composed of a membrane protein, lipids and two monomers of a "scaffold protein". The most used scaffold protein is an N-terminal truncation of apolipoprotein A-1 (apoA-1), which is the primary protein component of ...



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