While submitting a protein coding nucleotide sequence in genebank, some sequences are sent back to me saying that there are reading frameshift problem in that nucleotide sequence. How to detect reading frameshift and rectify my sequence before submitting to genebank? Are the any tool or softwares?
Is it because of bad nucleotide sequences at the end or in the middle of that sequence?
Is it necessary that while translating to amino acid sequences, position of the start codon should be at No. 1 of that sequences?
Kindly help me ...:)
Hi,
try ORF finder. Paste or load the sequence and it will find all possible ORF.
http://www.bioinformatics.org/sms2/orf_find.html
Hi Biswajit, concerning your last question: If you want to check the translation, you have to put the coding sequence start as 1 in most softwares, however some viewer suites e.g. MEGA4.0 will allow you to highlight any sequence - doing this with differing offset can help you find the start of your offending shift via back-search.
Following on Andrew's comment, you can make people even happier if you additionally check a hypothetical translation against known amino acid sequences from homologs. This way you can assign the correct start ATG and help minimize the appreciable amount of wrong CDS's databases sadly still contain, as sometimes the first ATG from a read is indiscriminately published as CDS.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biota
- Eukaryota
- Fungi