What is the difference between nucleotide representation in small letter and nucleotide representation in capital letter. For eg. What is the difference between AgAGACTA and AGAGACTA??
capital letters are used for translated protein seq. (GenBank format) and small letters used for nucleotide seq. (FASTA format)
all this for any sequece to be searched in NCBI
but when you go for SNPs
its different
lower case letter is used for sequence identified by RepeatMasker as repetitive or as low complexity
you can acess this information by accessing the refSNp page FASTa section and clicking on legent or following link
ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs782#fasta
thank u
Dear Priyanka
generally the capital letter nucleotide representation is found in FASTA format file, small letter is found when you will access any file in gene bank with gene ID or Acc. No.
for use in any software or online tool generally accept both format expect some of them like phylip etc
all the best
SAURABH GUPTA
When we look at RNAfrabase sequence data, few of the sequences represented as AgAGACTA. what does the "g" resemble in the sequence?
Hey!! As par my knowledge, small letters are generally used when there in an uncertainty in base calling.
capital letters are used for translated protein seq. (GenBank format) and small letters used for nucleotide seq. (FASTA format)
all this for any sequece to be searched in NCBI
but when you go for SNPs
its different
lower case letter is used for sequence identified by RepeatMasker as repetitive or as low complexity
you can acess this information by accessing the refSNp page FASTa section and clicking on legent or following link
ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs782#fasta
thank u
I agree with the previous two comments (by Pritish and Rajashri) ... the sequence representation depends on the context you are working on. I deal with a lot of gene-models and splicing so I generally represent the exons in UPPER CASE and introns in lower case for visual easyness.
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