The human chromosome DNA data in Ensembl release 96, here is in FASTA format.

Reading the Wikipedia article on the FASTA format, I understand the first line, prefixed with >, is variously referred to as a "comment" or "sequence headers". However, looking at FASTA files from different sources, it appears this first line is quite variable in actual content.

What are the colon separated fields in this FASTA header (as found above on the Ensemble FTP site)? Most fields are guessable, but an explanation of each field would be much appreciated. I believe the 46709983 is the number of base-pairs in the chromosome.

>21 dna:chromosome chromosome:GRCh38:21:1:46709983:1 REF

Finally, how should I have figured out the meaning of the header notation for myself? Is there a list of common or known header formats?


1 Answer 1


According to ensembl's website (albeit somewhat buried in a page about downloading data via FTP) it says:

"The header line in an FASTA dump files containing DNA sequence consists of the following attributes : coord_system:version:name:start:end:strand This coordinate-system string is used in the Ensembl API to retrieve slices with the SliceAdaptor."

A brief rundown of these attributes as I understand them:

  • coord_system- Is simply the coordinate system used to locate a particular feature within an assembly: "chromosome" and "BAC clone" are common examples as described here.
  • version- This is the current version of the assembly reference. And refers to an Ensembl archive as detailed here. (Yours appears to be from the human GRch38 assembly).
  • name- This seems pretty self explanatory. In this case we are looking at chromosome 21.
  • start- Again, self explanatory. Any complete chromosome or contiguous sequence is going to start at "1".
  • end- End of the fasta sequence. [start] - [end] + 1 = total length
  • strand- This refers to orientation (i.e. forward or reverse strand) 1 is forward (-1 is reverse)

Here is a link to a pdf containing this information and more about using Ensembl (see page 23)...

Unfortunately, to answer your final question, there is no easy way to come across this information and there are as many ways of labeling fasta files as there are sequence databases. Sequence repositories have come a long way in the last 10 years but there is still a lot of work to do toward standardizing data formats and making databases more user friendly.

  • $\begingroup$ Thanks David. I had looked at that page last week, in fact (it was helpful to know Ensembl supports rsync), but not read it closely enough, evidently. Cheers! $\endgroup$ Commented Jun 6, 2019 at 1:16
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    $\begingroup$ @RichardMichael fasta header can be anything. It is flexible because different fasta files would have different kinds of sequences. Therefore one standard will not suit them all. Moreover, fasta header is not really meant for annotation. If there is a GTF associated with the fasta then you will have the genomic co-ordinates and some other information (for e.g. the gene name) in the former. $\endgroup$
    Commented Jun 6, 2019 at 8:09

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