I have already found some simple sequence repeat (SSR) using MISA, SSRlocator tools on some gene sequence of human. Now I want to find the location of these SSRs, where the repeat located on the coding or non-coding (UTR) region of gene sequences, I can do it using USCS genome browser for one gene at the time, but it's time-consuming for many genes. Could you please let me know how I can perform it for many genes? Thanks
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updated 18 months ago by
Ram
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written 8.6 years ago by
seta
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what kind of simple sequence repeats ? do you want to process the sequences by yourself or do you want to know if any database knows about any repeat (poly-X, repeat-masker ? )
Actually, I have some simple sequence repeat (SSR) that would like to find their location on the gene sequences of interest, if repeats located on the coding or non-coding (UTR) regions?
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updated 18 months ago by
Ram
43k
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written 8.6 years ago by
seta
★
1.9k
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Entering edit mode
how do you check manually of the UTR contains a SSR ?
I have already find some SSR repeat using SSRlocator, MISA tools. Now, I want to know where is located these SSRs, on the coding or UTR parts of gene sequences of interest?
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updated 18 months ago by
Ram
43k
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written 8.6 years ago by
seta
★
1.9k
Thanks for your nice reply, however I have some predetermined SSR repeats, like AT, CCG, etc. Could you please let me know how I can find just repeats of interest?
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• link
updated 18 months ago by
Ram
43k
•
written 8.6 years ago by
seta
★
1.9k
what kind of simple sequence repeats ? do you want to process the sequences by yourself or do you want to know if any database knows about any repeat (poly-X, repeat-masker ? )
Actually, I have some simple sequence repeat (SSR) that would like to find their location on the gene sequences of interest, if repeats located on the coding or non-coding (UTR) regions?
how do you check manually of the UTR contains a SSR ?
I have already find some SSR repeat using SSRlocator, MISA tools. Now, I want to know where is located these SSRs, on the coding or UTR parts of gene sequences of interest?