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A sequence in biology is the one-dimensional ordering of monomers, covalently linked within a biopolymer; it is also referred to as the primary structure of a biological macromolecule. While it can refer to many different molecules, the term sequence is most often used to refer to a DNA sequence or a protein sequence .
However, comparing these new sequences to those with known functions is a key way of understanding the biology of an organism from which the new sequence comes. Thus, sequence analysis can be used to assign function to coding and non-coding regions in a biological sequence usually by comparing sequences and studying similarities and differences.
The initial scope of Biopython involved accessing, indexing and processing biological sequence files. While this is still a major focus, over the following years added modules have extended its functionality to cover additional areas of biology (see Key features and examples). As of version 1.77, Biopython no longer supports Python 2. [10]
However, it is sometimes desirable to sequence RNA molecules. While sequencing DNA gives a genetic profile of an organism, sequencing RNA reflects only the sequences that are actively expressed in the cells. To sequence RNA, the usual method is first to reverse transcribe the RNA extracted from the sample to generate cDNA fragments. This can ...
This does not imply a contradiction with the format as only the first line in a FASTA file may start with a ";" or ">", forcing all subsequent sequences to start with a ">" in order to be taken as separate sequences (and further forcing the exclusive reservation of ">" for the sequence definition line). Thus, the examples above would be a multi ...
Thus a consensus sequence is a model for a putative DNA binding site: it is obtained by aligning all known examples of a certain recognition site and defined as the idealized sequence that represents the predominant base at each position. All the actual examples shouldn't differ from the consensus by more than a few substitutions, but counting ...
Cis-regulatory DNA sequences that are located in DNA regions distant from the promoters of genes can have very large effects on gene expression, with some genes undergoing up to 100-fold increased expression due to such a cis-regulatory sequence. [3] These cis-regulatory sequences include enhancers, silencers, insulators and tethering elements. [4]
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal (or lateral) gene ...