PMC:5118421 / 5930-7455 JSONTXT

{"project":"TEST0","denotations":[{"id":"27920779-48-53-3100213","span":{"begin":207,"end":208},"obj":"[\"25634361\"]"},{"id":"27920779-139-145-3100214","span":{"begin":415,"end":417},"obj":"[\"9386342\", \"23671333\", \"5508247\"]"},{"id":"27920779-228-234-3100215","span":{"begin":1437,"end":1439},"obj":"[\"9386342\"]"}],"text":"A database of nucleic acid sequences for germline-encoded CDR1 and 2 and frameworks 1, 2, and 3 of functional Ig V-regions was extracted from www.ncbi.nlm.nih.gov/projects/igblast and compiled as described (2). All available mouse and human V genes were used in the analyses. Framework regions (FRs) and CDR sequences were defined using the Kabat and/or IMGT definitions as indicated in the text or figure legends (20–22). The framework regions (FRs) 1–3 or CDR1 and 2 sequences were fused to form a continuous sequence, and codon frequencies were calculated by the function provided at http://www.kazusa.or.jp/codon/. This approach was made possible by the fact that CDR and FR definitions begin and end with intact codons. IgVH genes from cartilaginous fishes were extracted from http://www.imgt.org/. All 12 functional genomic DNA sequences available at the time of the analyses were used to determine the average observed/expected ratios of AGY and TCN Ser codons among germline-encoded CDRs. The following sequences were used in the analyses: Ginglymostoma cirratum (IGHV2S1*01, IGHV2S2*01, IGHV2S3*01, and IGHV2S4*01), Heterodontus francisci (IGHV1S1*01, IGHV1S15*01, IGHV1S3*01, IGHV1S4*01), Leucoraja erinacea (IGHV1S3*01, IGHV1S4*01, and IGHV1S5*01), and Hydrolagus colliei (IGHV1S3*01). Nucleotide sequences encoding mouse TCRV-region CDRs (IMGT definition) were also extracted from functional V genes at http://www.imgt.org/ (20). In cases where a V gene had multiple alleles, the first listed allele was analyzed."}

{"project":"2_test","denotations":[{"id":"27920779-25634361-34707936","span":{"begin":207,"end":208},"obj":"25634361"},{"id":"27920779-9386342-34707937","span":{"begin":415,"end":417},"obj":"9386342"},{"id":"27920779-23671333-34707937","span":{"begin":415,"end":417},"obj":"23671333"},{"id":"27920779-5508247-34707937","span":{"begin":415,"end":417},"obj":"5508247"},{"id":"27920779-9386342-34707938","span":{"begin":1437,"end":1439},"obj":"9386342"}],"text":"A database of nucleic acid sequences for germline-encoded CDR1 and 2 and frameworks 1, 2, and 3 of functional Ig V-regions was extracted from www.ncbi.nlm.nih.gov/projects/igblast and compiled as described (2). All available mouse and human V genes were used in the analyses. Framework regions (FRs) and CDR sequences were defined using the Kabat and/or IMGT definitions as indicated in the text or figure legends (20–22). The framework regions (FRs) 1–3 or CDR1 and 2 sequences were fused to form a continuous sequence, and codon frequencies were calculated by the function provided at http://www.kazusa.or.jp/codon/. This approach was made possible by the fact that CDR and FR definitions begin and end with intact codons. IgVH genes from cartilaginous fishes were extracted from http://www.imgt.org/. All 12 functional genomic DNA sequences available at the time of the analyses were used to determine the average observed/expected ratios of AGY and TCN Ser codons among germline-encoded CDRs. The following sequences were used in the analyses: Ginglymostoma cirratum (IGHV2S1*01, IGHV2S2*01, IGHV2S3*01, and IGHV2S4*01), Heterodontus francisci (IGHV1S1*01, IGHV1S15*01, IGHV1S3*01, IGHV1S4*01), Leucoraja erinacea (IGHV1S3*01, IGHV1S4*01, and IGHV1S5*01), and Hydrolagus colliei (IGHV1S3*01). Nucleotide sequences encoding mouse TCRV-region CDRs (IMGT definition) were also extracted from functional V genes at http://www.imgt.org/ (20). In cases where a V gene had multiple alleles, the first listed allele was analyzed."}

{"project":"MyTest","denotations":[{"id":"27920779-25634361-34707936","span":{"begin":207,"end":208},"obj":"25634361"},{"id":"27920779-9386342-34707937","span":{"begin":415,"end":417},"obj":"9386342"},{"id":"27920779-23671333-34707937","span":{"begin":415,"end":417},"obj":"23671333"},{"id":"27920779-5508247-34707937","span":{"begin":415,"end":417},"obj":"5508247"},{"id":"27920779-9386342-34707938","span":{"begin":1437,"end":1439},"obj":"9386342"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"A database of nucleic acid sequences for germline-encoded CDR1 and 2 and frameworks 1, 2, and 3 of functional Ig V-regions was extracted from www.ncbi.nlm.nih.gov/projects/igblast and compiled as described (2). All available mouse and human V genes were used in the analyses. Framework regions (FRs) and CDR sequences were defined using the Kabat and/or IMGT definitions as indicated in the text or figure legends (20–22). The framework regions (FRs) 1–3 or CDR1 and 2 sequences were fused to form a continuous sequence, and codon frequencies were calculated by the function provided at http://www.kazusa.or.jp/codon/. This approach was made possible by the fact that CDR and FR definitions begin and end with intact codons. IgVH genes from cartilaginous fishes were extracted from http://www.imgt.org/. All 12 functional genomic DNA sequences available at the time of the analyses were used to determine the average observed/expected ratios of AGY and TCN Ser codons among germline-encoded CDRs. The following sequences were used in the analyses: Ginglymostoma cirratum (IGHV2S1*01, IGHV2S2*01, IGHV2S3*01, and IGHV2S4*01), Heterodontus francisci (IGHV1S1*01, IGHV1S15*01, IGHV1S3*01, IGHV1S4*01), Leucoraja erinacea (IGHV1S3*01, IGHV1S4*01, and IGHV1S5*01), and Hydrolagus colliei (IGHV1S3*01). Nucleotide sequences encoding mouse TCRV-region CDRs (IMGT definition) were also extracted from functional V genes at http://www.imgt.org/ (20). In cases where a V gene had multiple alleles, the first listed allele was analyzed."}