fasta sequence: 0 based or 1 based index

[ardmore]

When we say the position of a sequence, is zero based or one based?
Because I want to extract a sub sequence from a long one.

AGCTTT
012345

OR

AGCTTT
123456

Thanks.

[ffinkernagel]

That is undefined if you don't specify which system (or language) you're working with.

[ardmore]

Okay. If the sequence is given and a position 63150935 is given as well. I want to get 1000kb size around this point by C#.
Then

string trunk = sequence.Substring(63150935-500000,1000000);

or

string trunk = sequence.Substring(63150934-500000,1000000);

Which one is correct?

[ffinkernagel]

In c# the indices are 0 based, so the first one would be apppropriate if your position is also defined as 0 based.

If it was 1 based (for example, if it comes from Ensembl), you'll need to do the second one though.

[ardmore]

My question is not for C#. I meant that I am not sure whether the sequence is defined as 0 based or not. The sequence is a fasta file or extracted from a genome.

[ffinkernagel]

The sequence is not your issue. A sequence itself is not '0 based', it's just a list of characters.
Where does your position 63150935 come from?

[ardmore]

It is from a bam file output. If we define a region such as chr22:10000-20000.
And we get the consensus sequence, we only interest one small region around a specific position.
How to?

[gringer]

If it's from a BAM/SAM file, then look at the BAM/SAM specification:

http://samtools.sourceforge.net/SAM1.pdf

For example, the fourth field of SAM files is 1-based:

POS: 1-based leftmost mapping POSition of the first matching base. The first base in a reference
sequence has coordinate 1. POS is set as 0 for an unmapped read without coordinate. If POS is
0, no assumptions can be made about RNAME and CIGAR.

whereas the internal BAM representation is 0-based:

pos / 0-based leftmost coordinate (= POS − 1) / int32 t / [-1]

[ardmore]

Thank you.