Update hlall.fa or hla.clean.fasta

[Daniel Eriksson]

Dear group members,

I have tried to assemble an update of hlall.fa (hla.clean.fasta) but downloading and merging the gen.fasta-files from IMGT generates a much smaller file than the original supplied with the ATHLATES download. Are there any instructions on how this can be done properly? How do you update the reference?

Here are the fasta-files I have been trying to merge:

ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/

Thank you for your kind help!

[bmp1...@student.lu.se]

Hi,

I also had the same question a few days ago. 

However the hla.clean.fasta file contains both the gen.fasta files and nuc.fasta files.

I prepared the hlaall.fa by merging all of these files. In this way I got 15035 sequence-headers. 

hla.clean.fasta : 7.4 Mb, 8230 sequence headers

merged fasta (.nuc +.gen):  13 Mb,15035 sequence headers

Does this answer your question? 

[Daniel Eriksson]

Yes, this solves the problem. Thank you.

It seemed to me that some, a few, nuc/gen sequences are identical. To get athlates running I had to remove the duplicates. 

Thank you again!

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