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6

OK, first of all do not use CLustalX to align the sequences. It is a very old algorithm and is outperformed by just about any modern aligner (including its descendent, clustal omega, and t-coffee, mafft, kalign etc etc). As for 1) that depends on what you want to do, there is no perfect solution. What question are you trying to answer? If you want a tree ...


4

Ribosomes are the only means we know by which cells produce proteins. Consequently, all proteins are made by a ribosome, including the proteins that then become part of a new ribosome. It's never a question of "more proteins than required" because there are different types of proteins and to make a ribosome, you need those specific types of proteins known as ...


4

As indicated in the comments there are several non-coding (untranslated) RNAs, that the cell produces. Most of these perform gene regulatory functions. However, widespread transcription is known to take place throughout the genome (pervasive transcription), but the functions of these RNAs are not clearly understood. It has been suggested that in certain ...


2

Untranslated RNA is incredibly important. As mentioned it regulates gene control, siRNA or miRNA for example can cut up mRNA preventing it being translated. Others can cause an increase in expression like enhancer RNA. Then RNA can act as tRNA or ribosomal RNA in protein translation. RNA can be enzymatically active, RNA also acts as a primer for initiation ...


2

Generally most organisms have multiple copies of the genes/regions coding for ribosomal RNA (since it's needed quite a lot). Additionally these regions can be repetitive or otherwise similar to sequence or place correctly in the genome, therefore it's generally harder to find good genomic sequences for rRNA compared to other genes. Based on your link, it ...


2

RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database http://www.rnasoft.ca/strand/ 16S rRNA: secondary structure file in ct format http://www.rnasoft.ca/strand/show_file.php?format=CT&molecule_ID=CRW_00111&check_out_the=View+the+RNA+sequence+and+secondary+structure+for+molecule+CRW_00111 5S rRNA: secondary structure ...


2

In general, you extract DNA, then PCR out the 16rRNA coding regions and finally sequence them. Here some links http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/16s/ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068739 https://support.illumina.com/content/dam/illumina-marketing/documents/products/other/16s-metagenomics-...


2

It is not conserved, its sequence is not the same in all bacteria. Indeed, it has a slow rate of evolution (mutation) that make it perfect to build phylogenetic trees. As correctly suggested by David in his comment, here are some references about the 16s rRNA and on how it is used to identify known and unknown bacteria. http://www.sciencedirect.com/science/...


2

The three RNA polymerases (RNAPs) are very similar to each other, yet not identical. As described in this article, there are subunits that are specific for each type of polymerases. In addition to providing unique substrates that polymerase-specific subunits bind to give each of the RNAPs their specific functionality, the two largest subunits also shape ...


1

When cells are not producing proteins they are performing their specialized functions. Consider red blood cells carrying oxygen. Or gut epithelial cells aiding in your digestion. The list goes on...liver cells have a different role than the keratin cells in your hair. There is a lot of transport that goes on as well in an certain cells that is carried ...


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