what does this header mean?
If I want to randomly pick 10 sequences (30 in length) from the .fasta file to generate another .fasta file for testing, what does mean by
"put the zero-based location of the mRNA transcript from where the read is taken" and ">NM_001008503.1:coordinate_of_read....."?
The file I uploaded is the sample .fasta file I am gonna use.
With the NM number you can get more informations about the mRNA, see:
http://www.ncbi.nlm.nih.gov/nuccore/NM_001008503.1
NM_001008503.1:237:1493:1576
1. NM_XXXX, this is the NCBI RefSeq identifier for an mRNA (protein would be "NP"). See here: http://www.ensembl.org/info/docs/genebuild/genome_annotation.html. "N" in this case means that it is a manually reviewed and annotated sequence.
2. The rest is not standard. (where do you have the sequences from?). The last number obviously indicates the last position in the sequence in a zero-based notation (the length of the sequence would be this number plus one). I assume that the two other numbers are related to a second gen sequencing run (position of the reads).
3. The zero based notation: first letter in the sequence is at position "0", second is at position "1" etc. Thus, a three-letter sequence has length 3, and the last position is 2.
thanks very much for all your answers.
the reads were picking from NCBI by python script, and ".1:237:1493:1576" are the version, cds, length of the sequence.
the .fasta file were made by the reads and headers picked by the python script, that is why i couldn't find information of the header on similar format.
http://www.ncbi.nlm.nih.gov/nuccore/NM_001008503.1
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