Comments (3)
AlsoATraveler
commented on August 16, 2024
The same is A*01:01:02, and TGGAGAACGGGAAGGAGACGCTGCAGCGCACGGA, which is TGGAGAACGGGAAGGAGACGCTGCAGCGCACGGG in A_gen.fasta
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dominicbarkerAN
commented on August 16, 2024
Hello, I have reviewed the sequence you have suggested and found no issue with it. The sequence in 3.40.0 is the same as the sequence in the latest release, which is correct. The issue that you are having is that you are not correctly splitting the CDS sequence in the A_nuc.fasta file into exons to search for it in the A_gen.fasta, which contains exons and introns.
For example you say that the A_nuc.fasta file ends AAAGTGTGA which does not appear in the A_gen.fasta. That is because this sequence you are searching for covers two exons, the end of exon 7 and exon 8. It would not appear in the A_gen.fasta because of the intron 7 sequence between these two. The exon 7 and exon 8 sequence of A*01:01:02 is:
exon 7: GCAGTGACAGTGCCCAGGGCTCTGATGTGTCTCTCACAGCTTGTAAAG
exon 8: TGTGA
The same is true for your second comment which contains sequence crossing exon 3 and 4.
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AlsoATraveler
commented on August 16, 2024
Oh, thanks.
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Related Issues (20)
- Alignments missing most of sequence HOT 2
- The DPA2 and DPB2 nucleotide alignments include codon numbering but have no cognate peptide alignments HOT 2
- An unexpected change in hla.xml format HOT 3
- 3.54.0 release tag HOT 8
- HLA01143,B*27:18
- Hi.dear
- Release version as JSON and/or XML HOT 4
- Block of allele names with no associated sequences in the HLA-A protein alignment in release 3.55.0 HOT 2
- Discrepancy between TAP2 protein and nucleotide alignments HOT 3
- Discrepancy between the DPA1_prot.txt and DPA1_nuc.txt files for the DPA1*03:05:01Q alleles HOT 4
- The DPA1*01:05 allele is missing from the DPA1 genomic alignment. HOT 3
- HLA-DOB*01:04:01:02 region annotation HOT 2
- not found HLA39951,DRB3*03:70 genomic sequence in fasta folder HOT 7
- how to use the latet IMGT to create PRG_MHC_GRCh38_withIMGT database from HLA-LA typing tool ? HOT 1
- hla.dat File sequence version changes HOT 2
- wmda rel_dna_ser.txt description HOT 1
- Typo in the URL for the /alignments directory in release/branch 3.17.0. HOT 2
- A list of HLA-B alleles and its corresponding B leader genotypes. HOT 1
- Incorrect id in alignmentreference element HOT 1
- The nucleotide alignment for the HLA-R gene fragment includes extraneous AA codon lines HOT 2
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