I have some amplified sequences of ribosomal DNA which contain 28S rRNA, ITS1, 5.8s rRNA, ITS2 and 28S rRNA, but I dont know to how to find the starting and ending position of each region seprately. I have seen on NCBI that some of already submitted sequeces show the starting and ending position of these region within the sequence when I clicked on graphics. Can anybody suggest the software and/or working procedure to resolve this problem. Thanks in advance.
The easiest way is to align your sequences with other published on NCBI for close related species. The ITSs are more variable but the ribosomal genes are highly conserved, and you should be able to align the initial and last nucleotides of the genes to other organisms of the same Family.
You will also notice that ITSs are usually much more rich in AT, while the genes have higher GC content.
CLUSTAL W2 is a free online software for alignments.
Good luck!
http://www.ebi.ac.uk/Tools/msa/clustalw2/
Maria A. Zuriaga its not abut the alignment of f sequences, its about the positioning of all the above said region within the sequences. For example; I have a sequence with a length of 761 bases (ATGC) which start with 18S, ITS1-5.8S-ITS2 and end with 28S rRNA. But i do not know about the position and length of each region and starting and ending position of all the region. Can you suggest me for same?
Sorry, I don't understand your question. Aligning with known sequences of close related organisms will help you see where the genes and ITSs start and end, other that that, I don't know what you mean...
This is a fairly old post so perhaps you already found this: http://www.sciencedirect.com/science/article/pii/S0378111908005374
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