If i have a sequence of the nrDNA that contains different genes. how can i determined the exact sequence of each gene or spacer?
The sequences of my fungal species were obtained from amplicons (the PCR was done using ITS-1 and ITS4B primers).
The sequences contain 18S rRNA, ITS1, 5.8S rRNA, ITS2.
If any tool that may help?
If i have a refrence sequence for the genus, could i depend on it to determine the begin and the end of the genes and spacer??
Thanks,
You should ideally perform BLAST analysis at NCBI. Then retrieve accession of closely related hits and mark the 18S rRNA, ITS1, 5.8S rRNA, ITS2 in those reference sequence. Further download those sequences (five to ten) and perform clustalw alignment. You can mark out 18S rRNA, ITS1, 5.8S rRNA, ITS2 sequences in your sample sequence. This can help you annotate and mark spacer sequence in sequence data obtained for your culture.
Thanks very much for your answer, I have already performed BLAST analysis and just wanted to get sure or to find more reliable method.
You can use ITSx software (http://microbiology.se/software/itsx/) to extract ITS1 and ITS2 regions of your sequences, and also gives you a list with the nucleotides that are for each region for each sequence.
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