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I will try to answer the question in the title: how can we know the sites where DNA binding proteins bind? I'll explain two experimental methods to identify binding sites on DNA. DNase footprinting ChIP-seq (Chromatin Immuno-Precipitation with sequencing) DNase footprinting We can locate proteins bound to DNA by their ability to protect DNA from some ...


6

CCCEEE etc. are the secondary structural elements. The C or E usually refers to whether the residue is coiled (C) or part of a strand (E). H would be used to denote a helix. However in this case the C refers to non-strand and non-helix regions i.e looping regions rather than a coiled region (although I think this is more of a point of semantics). e or - ...


4

http://phylot.biobyte.de/ performs the requisite task (generating a phylogenetic tree based on the specific organisms provided, using the NCBI taxonomy tables). For example, the input of tree elements Trichomonas vaginalis,Trypanosoma brucei,Homo sapiens,Fibroporia radiculosa,Paramecium tetraurelia,Tetrahymena thermophila,Cryptosporidium ...


4

I would do this through the Reactome database. Searching for "AKT Signalling" returns, among other things, an entry for PI3K/AKT Signaling in Cancer (Homo sapiens) (REACT_147723). Clicking on that link will take you to the pathway's page, and if you click on "Disease" (under "Locations in the PathwayBrowser"), you will be shown a link to the pathway browser ...


3

is the pseduoknot the alignment of these base pairs I'm not exactly sure what is meant by alignment, but if you mean base pairing from the flanking RNA to the loop of the hairpin you have depicted, then you would have an H-type pseudoknot. Since you are interested in predicting these structures, it's important to note that a nucleic acid sequence ...


2

The European Bioinformatics Institute (EBI) has a tool called "Quick GO", which allows you to search the Gene Ontology (GO) database using specific pathways or terms. In the "Annotation Download" section (http://www.ebi.ac.uk/QuickGO/GAnnotation) enter your search term (e.g. "AKT signalling") and "search". QuickGO will present you with the search results, ...


2

CDS is based on ORF prediction and unless the protein product is known it is classified as an mRNA for a hypothetical protein (Refseq id: XM_*). As Devon Ryan said sometimes UTR ends are not accurately annotated. If you are interested in finding the 3' end of 5'UTR then the problem is basically to find the translation start site. You can have a look at ...


1

If what you want is to find a consensus structure for a group of alignments in stockholm format then you might try with RNAalifold and for single sequence folding check RNAfold. Both have online servers and can also be run offline. After you get the consensus structure update the stockholm file by adding a structure consensus line as: #=GC SS_cons ...


1

As WYSIWYG touches on in the comments, usually dashes mean that there are gaps in the alignment (an artefact of a deletion or addition mutation perhaps) and the dots are used to show point mutations where the biochemical properties are mostly conserved, but the residue has changed. From original question, not relevant to question as it stands. You are ...


1

Comparing Protein Structures There are a number of things you can look at such as root mean square deviation. This method compares the co-ordinates of two structures by superposing them on top of each other. RMSD: This is implemented in the modelling Modeller or can be used in USCF Chimera RMSD will provide a number in angstroms squared, with higher ...


1

It depends on how accurate you want the description to be. Ideal bond lengths are normally assumed, so the structure can be described using φ, ψ, ω (for the backbone) and χ1-χ5 (for the sidechain) angles. This is what is used in most cases. However, the positions of the hydrogens in the sidechains are not uniquely defined by this description. This also does ...



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