I found a fasta file (which I must analyse) with some identifiers and information I don't know what does it mean completely.
>NM_001103386.01.e12_cds11 chrX 23878 11577 11716 FWD(+) 140bp frame: 1
>NM_001014709.01.i03_cds02-cds03 chrX 173667 6453 6751 REV(-) 299bp frame: 0
The first part is a gene identifier from NCBI (NM_001103386), the some obscure cds identifiers, chromosome, position of something, start and end positions of the feature on that chromosome. If it is forward or reverse, the length (subtracting the end minus the start) and the frame.
But how do I use this?
I am trying to extract the feature from the sequence, I thought I should use the frame number on the sequence and the FWD and REV to select the right sequence. But now I thought it could already be that the whole sequence is already the feature. Anyone knows where could these data come? Or if I should use the whole sequence as is or I should find the right strand and find the right frame?
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Where did this file come from?
Edit: Those accession numbers are for Drosophila.
But this part is not making sense:
chrX 23878 11577 11716NM_001103386 is on chr X but it is not in the in the region indicated by the start (?) 23878.
RhoGAP1A-RB (Fruitfly Transcript)
Thats my main problem I don't know where do they come from and I can't retrieve a new set (it is part of an exercise), so I thought if anyone could guess what does it really mean. If I could know where does it come from I could know what's the meaning of the lines.
Do you have to analyze the sequence or the header? Forget about the header, focus on the sequence.
Original post indicates that he needs to extract "the feature" (I assume described in the header) from the same (or some other) sequence.
That was the answer of my professor who couldn't remember where did he take the sequences. But thanks anyway
Analyzing data you don't understand is like a fools errand. Especially if you need to extract information that is not described.
I think what you have in the fasta header are are blast hit information munged into it.
Frankly I think you should take this back to whoever gave it to you and explain that solving this is not actual science but guesstimating and you are wasting time solving it.
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