How to split fasta nucleotide sequence Into Coding And Noncoding region?

Question

[bioinform_1]

Hi,

I have two question.

1. How to split fasta nucleotide sequence (concatenated) Into two files a) Coding And b) Noncoding region?

2. How to include charsets range in nex file for concatenated fasta nucleotide sequence?

Any help would be greatly appriciated.

Thanks Shree

Answer 1

[Asaf]

1. bedtools getfasta You just need the coding and noncoding as a bed file

[bioinform_1]

These are concatenated fasta file of 200 genes (Gblocked). How do i get the coding and noncoding region??

How to include charsets range in nex file for concatenated fasta nucleotide sequence?

Thanks

[Asaf]

What do you mean by gene? (DNA/protein/CDS only/spliced...)

[bioinform_1]

The fasta file are aligned DNA sequence and were Gblocked to remove poorly aligned region and were concatenated.

[Asaf]

Do you know which regions are coding then? Do you have this information on one of the sequences? I'm trying to understand your input

[bioinform_1]

I do not know the coding regions. These are orthologous DNA sequence (200) aligned with prank, Gblocked to remove poorly aligned region and concatenated with FASconCAT.

[Asaf]

And what is the origin of the 200 bp? If you don't know you might want to map them to a file of coding sequence and then extract the coding/non-coding

[bioinform_1]

These are 200 genes. After alignment, poorly aligned regions were removed. The concatenated size is 2200 kb.

[Asaf]

If you'll know what the input is (where the coding regions are) you might be able to extract the sequences, if you don't know that what's your plan?