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CHERRY-ui8ChenZiHong-Gavin
CHERRY-ui8
and
ChenZiHong-Gavin
authored
add: search multi omics (#140)
* refactor: reconstruct examples/search file * feat: enhance BaseSearcher * feat: enhance searchers with multi-threading and improved error handling * add: add searched example input files for DNA, protein, and RNA * refactor: replace search_all with SearchService * fix: update search operator init to use SearchService * fix: upgrade run_concurrent to be compactible with SearchService * fix: add undefined functions in DNA db building script * perf: perf search_service * wip: add pipeline annotations * refactor: update multi-omcis eg. input to use specific data types * refactor: update input format in README files and base_reader * chore: add kv_backend and graph_backend params to search config files * refactor: implement lazy imports in BaseOperator to avoid circular dependencies * refactor: remove unnecessary asyncio locks and thread pool in searchers * refactor: update SearchService to use specific search classes, implement async search wrapper and remove unnecessary search output keys * style: fix pylint problems * fix: change async BaseSearcher to sync to match DNA, RNA and protein searchers * fix: pass threshold in searcher config * fix: delete duplicate logger * perf: perf search service * Merge branch 'main' of https://github.com/open-sciencelab/GraphGen into search-multi-omics * fix: fix pylint problems (extract sequence parsing and local search logic of RNA and prot search) --------- Co-authored-by: chenzihong-gavin <[email protected]> Co-authored-by: chenzihong <[email protected]>
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‎examples/input_examples/search_dna_demo.jsonl‎

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{"type": "text", "content": "NG_033923"}
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{"type": "text", "content": "NG_056118"}
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{"type": "text", "content": ">query\nACTCAATTGTCCCAGCAGCATCTACCGAAAAGCCCCCTTGCTGTTCCTGCCAACTTGAAGCCCGGAGGCCTGCTGGGAGGAGGAATTCTAAATGACAAGTATGCCTGGAAAGCTGTGGTCCAAGGCCGTTTTTGCCGTCAGCAGGATCTCCAGAACCAAAGGGAGGACACAGCTCTTCTTAAAACTGAAGGTATTTATGGCTGACATAAAATGAGATTTGATTTGGGCAGGAAATGCGCTTATGTGTACAAAGAATAATACTGACTCCTGGCAGCAAACCAAACAAAACCAGAGTAAGGTGGAGAAAGGTAACGTGTGCCCACGGAAACAGTGGCACAATGTGTGCCTAATTCCAAAGCAGCCGTCCTGCTTAGGCCACTAGTCACGGCGGCTCTGTGATGCTGTACTCCTCAAGGATTTGAACTAATGAAAAGTAAATAAATACCAGTAAAAGTGGATTTGTAAAAAGAAAAGAAAAATGATAGGAAAAGCCCCTTTACCATATGTCAAGGGTTTATGCTG"}
4-
{"type": "text", "content": "ACTCAATTGTCCCAGCAGCATCTACCGAAAAGCCCCCTTGCTGTTCCTGCCAACTTGAAGCCCGGAGGCCTGCTGGGAGGAGGAATTCTAAATGACAAGTATGCCTGGAAAGCTGTGGTCCAAGGCCGTTTTTGCCGTCAGCAGGATCTCCAGAACCAAAGGGAGGACACAGCTCTTCTTAAAACTGAAGGTATTTATGGCTGACATAAAATGAGATTTGATTTGGGCAGGAAATGCGCTTATGTGTACAAAGAATAATACTGACTCCTGGCAGCAAACCAAACAAAACCAGAGTAAGGTGGAGAAAGGTAACGTGTGCCCACGGAAACAGTGGCACAATGTGTGCCTAATTCCAAAGCAGCCGTCCTGCTTAGGCCACTAGTCACGGCGGCTCTGTGATGCTGTACTCCTCAAGGATTTGAACTAATGAAAAGTAAATAAATACCAGTAAAAGTGGATTTGTAAAAAGAAAAGAAAAATGATAGGAAAAGCCCCTTTACCATATGTCAAGGGTTTATGCTG"}
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{"type": "dna", "content": "NG_033923"}
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{"type": "dna", "content": "NG_056118"}
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{"type": "dna", "content": ">query\nACTCAATTGTCCCAGCAGCATCTACCGAAAAGCCCCCTTGCTGTTCCTGCCAACTTGAAGCCCGGAGGCCTGCTGGGAGGAGGAATTCTAAATGACAAGTATGCCTGGAAAGCTGTGGTCCAAGGCCGTTTTTGCCGTCAGCAGGATCTCCAGAACCAAAGGGAGGACACAGCTCTTCTTAAAACTGAAGGTATTTATGGCTGACATAAAATGAGATTTGATTTGGGCAGGAAATGCGCTTATGTGTACAAAGAATAATACTGACTCCTGGCAGCAAACCAAACAAAACCAGAGTAAGGTGGAGAAAGGTAACGTGTGCCCACGGAAACAGTGGCACAATGTGTGCCTAATTCCAAAGCAGCCGTCCTGCTTAGGCCACTAGTCACGGCGGCTCTGTGATGCTGTACTCCTCAAGGATTTGAACTAATGAAAAGTAAATAAATACCAGTAAAAGTGGATTTGTAAAAAGAAAAGAAAAATGATAGGAAAAGCCCCTTTACCATATGTCAAGGGTTTATGCTG"}
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{"type": "dna", "content": "ACTCAATTGTCCCAGCAGCATCTACCGAAAAGCCCCCTTGCTGTTCCTGCCAACTTGAAGCCCGGAGGCCTGCTGGGAGGAGGAATTCTAAATGACAAGTATGCCTGGAAAGCTGTGGTCCAAGGCCGTTTTTGCCGTCAGCAGGATCTCCAGAACCAAAGGGAGGACACAGCTCTTCTTAAAACTGAAGGTATTTATGGCTGACATAAAATGAGATTTGATTTGGGCAGGAAATGCGCTTATGTGTACAAAGAATAATACTGACTCCTGGCAGCAAACCAAACAAAACCAGAGTAAGGTGGAGAAAGGTAACGTGTGCCCACGGAAACAGTGGCACAATGTGTGCCTAATTCCAAAGCAGCCGTCCTGCTTAGGCCACTAGTCACGGCGGCTCTGTGATGCTGTACTCCTCAAGGATTTGAACTAATGAAAAGTAAATAAATACCAGTAAAAGTGGATTTGTAAAAAGAAAAGAAAAATGATAGGAAAAGCCCCTTTACCATATGTCAAGGGTTTATGCTG"}

‎examples/input_examples/search_protein_demo.jsonl‎

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{"type": "text", "content": "P01308"}
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{"type": "text", "content": "P68871"}
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{"type": "text", "content": "P02768"}
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{"type": "text", "content": "P04637"}
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{"type": "text", "content": "insulin"}
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{"type": "text", "content": "hemoglobin"}
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{"type": "text", "content": "p53"}
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{"type": "text", "content": "BRCA1"}
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{"type": "text", "content": "albumin"}
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{"type": "text", "content": "MHHHHHHSSGVDLGTENLYFQSNAMDFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDANMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQALKQLAEQSLDTSALEALADYIIQRNK"}
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{"type": "text", "content": "MGSSHHHHHHSQDLENLYFQGSMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRTKRVITTFRTGTWDAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV"}
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{"type": "text", "content": "MAKREPIHDNSIRTEWEAKIAKLTSVDQATKFIQDFRLAYTSPFRKSYDIDVDYQYIERKIEEKLSVLKTEKLPVADLITKATTGEDAAAVEATWIAKIKAAKSKYEAEAIHIEFRQLYKPPVLPVNVFLRTDAALGTVLMEIRNTDYYGTPLEGLRKERGVKVLHLQA"}
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{"type": "text", "content": "MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR"}
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{"type": "text", "content": "GSHMLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIVPSAQ"}
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{"type": "protein", "content": "P01308"}
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{"type": "protein", "content": "P68871"}
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{"type": "protein", "content": "P02768"}
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{"type": "protein", "content": "P04637"}
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{"type": "protein", "content": "insulin"}
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{"type": "protein", "content": "hemoglobin"}
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{"type": "protein", "content": "p53"}
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{"type": "protein", "content": "BRCA1"}
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{"type": "protein", "content": "albumin"}
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{"type": "protein", "content": "MHHHHHHSSGVDLGTENLYFQSNAMDFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDANMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQALKQLAEQSLDTSALEALADYIIQRNK"}
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{"type": "protein", "content": "MGSSHHHHHHSQDLENLYFQGSMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRTKRVITTFRTGTWDAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV"}
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{"type": "protein", "content": "MAKREPIHDNSIRTEWEAKIAKLTSVDQATKFIQDFRLAYTSPFRKSYDIDVDYQYIERKIEEKLSVLKTEKLPVADLITKATTGEDAAAVEATWIAKIKAAKSKYEAEAIHIEFRQLYKPPVLPVNVFLRTDAALGTVLMEIRNTDYYGTPLEGLRKERGVKVLHLQA"}
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{"type": "protein", "content": "MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR"}
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{"type": "protein", "content": "GSHMLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIVPSAQ"}

‎examples/input_examples/search_rna_demo.jsonl‎

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{"type": "text", "content": "hsa-let-7a-1"}
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{"type": "text", "content": "XIST regulator"}
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{"type": "text", "content": "URS0000123456"}
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{"type": "text", "content": "URS0000000001"}
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{"type": "text", "content": "URS0000000787"}
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{"type": "text", "content": "GCAGTTCTCAGCCATGACAGATGGGAGTTTCGGCCCAATTGACCAGTATTCCTTACTGATAAGAGACACTGACCATGGAGTGGTTCTGGTGAGATGACATGACCCTCGTGAAGGGGCCTGAAGCTTCATTGTGTTTGTGTATGTTTCTCTCTTCAAAAATATTCATGACTTCTCCTGTAGCTTGATAAATATGTATATTTACACACTGCA"}
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{"type": "text", "content": ">query\nCUCCUUUGACGUUAGCGGCGGACGGGUUAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCGAACCGCAUGGUUCGAUAGUGAAAGAUGGUUUUGCUAUCACUUAUAGAUGGACCCGCGCCGUAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCGACGAUACGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGGGG"}
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{"type": "text", "content": "CUCCUUUGACGUUAGCGGCGGACGGGUUAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCGAACCGCAUGGUUCGAUAGUGAAAGAUGGUUUUGCUAUCACUUAUAGAUGGACCCGCGCCGUAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCGACGAUACGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGGGG"}
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{"type": "rna", "content": "hsa-let-7a-1"}
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{"type": "rna", "content": "XIST regulator"}
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{"type": "rna", "content": "URS0000123456"}
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{"type": "rna", "content": "URS0000000001"}
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{"type": "rna", "content": "URS0000000787"}
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{"type": "rna", "content": "GCAGTTCTCAGCCATGACAGATGGGAGTTTCGGCCCAATTGACCAGTATTCCTTACTGATAAGAGACACTGACCATGGAGTGGTTCTGGTGAGATGACATGACCCTCGTGAAGGGGCCTGAAGCTTCATTGTGTTTGTGTATGTTTCTCTCTTCAAAAATATTCATGACTTCTCCTGTAGCTTGATAAATATGTATATTTACACACTGCA"}
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{"type": "rna", "content": ">query\nCUCCUUUGACGUUAGCGGCGGACGGGUUAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCGAACCGCAUGGUUCGAUAGUGAAAGAUGGUUUUGCUAUCACUUAUAGAUGGACCCGCGCCGUAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCGACGAUACGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGGGG"}
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{"type": "rna", "content": "CUCCUUUGACGUUAGCGGCGGACGGGUUAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCGAACCGCAUGGUUCGAUAGUGAAAGAUGGUUUUGCUAUCACUUAUAGAUGGACCCGCGCCGUAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCGACGAUACGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGGGG"}

‎examples/input_examples/searched_dna_demo.jsonl‎

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{"_doc_id":"doc-NG_011079","type":"dna","content":"Title: Homo sapiens ribosomal protein L35a pseudogene 6 (RPL35AP6) on chromosome 1\nSequence: ACTCAATTGTCCCAGCAGCATCTACCGAAAAGCCCCCTTGCTGTTCCTGCCAACTTGAAGCCCGGAGGCCTGCTGGGAGGAGGAATTCTAAATGACAAGTATGCCTGGAAAGCTGTGGTCCAAGGCCGTTTTTGCCGTCAGCAGGATCTCCAGAACCAAAGGGAGGACACAGCTCTTCTTAAAACTGAAGGTATTTATGGCTGACATAAAATGAGATTTGATTTGGGCAGGAAATGCGCTTATGTGTACAAAGAATAATACTGACTCCTGGCAGCAAACCAAACAAAACCAGAGTAAGGTGGAGAAAGGTAACGTGTGCCCACGGAAACAGTGGCACAATGTGTGCCTAATTCCAAAGCAGCCGTCCTGCTTAGGCCACTAGTCACGGCGGCTCTGTGATGCTGTACTCCTCAAGGATTTGAACTAATGAAAAGTAAATAAATACCAGTAAAAGTGGATTTGTAAAAAGAAAAGAAAAATGATAGGAAAAGCCCCTTTACCATATGTCAAGGGTTTATGCTG","data_source":"ncbi","molecule_type":"DNA","database":"NCBI","id":"NG_011079","gene_name":"RPL35AP6","gene_description":"ribosomal protein L35a pseudogene 6","organism":"Homo sapiens","url":"https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/NG_011079","gene_synonyms":["RPL35A_3_191"],"gene_type":"other","chromosome":"1","genomic_location":"1-522","function":null,"title":"Homo sapiens ribosomal protein L35a pseudogene 6 (RPL35AP6) on chromosome 1","sequence":"ACTCAATTGTCCCAGCAGCATCTACCGAAAAGCCCCCTTGCTGTTCCTGCCAACTTGAAGCCCGGAGGCCTGCTGGGAGGAGGAATTCTAAATGACAAGTATGCCTGGAAAGCTGTGGTCCAAGGCCGTTTTTGCCGTCAGCAGGATCTCCAGAACCAAAGGGAGGACACAGCTCTTCTTAAAACTGAAGGTATTTATGGCTGACATAAAATGAGATTTGATTTGGGCAGGAAATGCGCTTATGTGTACAAAGAATAATACTGACTCCTGGCAGCAAACCAAACAAAACCAGAGTAAGGTGGAGAAAGGTAACGTGTGCCCACGGAAACAGTGGCACAATGTGTGCCTAATTCCAAAGCAGCCGTCCTGCTTAGGCCACTAGTCACGGCGGCTCTGTGATGCTGTACTCCTCAAGGATTTGAACTAATGAAAAGTAAATAAATACCAGTAAAAGTGGATTTGTAAAAAGAAAAGAAAAATGATAGGAAAAGCCCCTTTACCATATGTCAAGGGTTTATGCTG","sequence_length":522,"gene_id":"100271312","molecule_type_detail":"genomic region","_search_query":"ACTCAATTGTCCCAGCAGCATCTACCGAAAAGCCCCCTTGCTGTTCCTGCCAACTTGAAGCCCGGAGGCCTGCTGGGAGGAGGAATTCTAAATGACAAGTATGCCTGGAAAGCTGTGGTCCAAGGCCGTTTTTGCCGTCAGCAGGATCTCCAGAACCAAAGGGAGGACACAGCTCTTCTTAAAACTGAAGGTATTTATGGCTGACATAAAATGAGATTTGATTTGGGCAGGAAATGCGCTTATGTGTACAAAGAATAATACTGACTCCTGGCAGCAAACCAAACAAAACCAGAGTAAGGTGGAGAAAGGTAACGTGTGCCCACGGAAACAGTGGCACAATGTGTGCCTAATTCCAAAGCAGCCGTCCTGCTTAGGCCACTAGTCACGGCGGCTCTGTGATGCTGTACTCCTCAAGGATTTGAACTAATGAAAAGTAAATAAATACCAGTAAAAGTGGATTTGTAAAAAGAAAAGAAAAATGATAGGAAAAGCCCCTTTACCATATGTCAAGGGTTTATGCTG"}
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{"_doc_id":"doc-NG_033923","type":"dna","content":"Title: Callithrix jacchus immunity-related GTPase family, M, pseudogene (IRGMP) on chromosome 2\nSequence: GAACTCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAATGCCAGGATTACAGGTATGAGCCACCACGCCCAGCCAGCATTGGGGTATATCGAAGGCAGAGGTCATGAATGTTGAGAGAGCCTCAGCAGATGGGGACTTGCCAGAGGTGGTCTCTGCCATCAAGGAGAGTTTGAAGATAGTGTTCAGGACACCAGTCAACATCGCTATGGCAGGGGACTCTGGCAATAGCATATCCACCTTCATCAGTGCACTTCAAATCGCAGGGCATGAGGCGAAGGCCTCACCTCCTACTGGGCTGGTAAAAGCTACCCAAAGATGTGCCTCCTATTTCTCTTCCCGCTTTCCAAATGTGGTGCTGTGGGATCTGCCTGGAGCAGGGTCTGCCACCAAAACTCTGGAGAACTACCTGATGGAAATGTAGTTCAACCAATATGACTTCATCATGGTTGCATCTGCACAATTCAGCATGAATCATGTGATCCTTGCCAAAACCATTGAGGACATGGGAAAGAAGTTCTACATTGTCTGGACCAAGCTGGACATGGATCTCAGCACAGGTGCCCTCCCAGAAGTGCAGCTACTGTAAATCAGAGAAAATGTCCTGGAAAGTCTCCAGAGGGAGCAGGTATGTGAACTCCCCATATTTATGGCCTCCAGCCTTGAACCTTTATTGCATGACTTCCCAAAGCTTAGAGACACATTGCAAAAGACTCATCCAAATTAGGTGCCATGGCCCTCTTCAAAACCTGTCCCACACCTGTGAGATGATCACGAATGACAAAGCAATCTCCCTGCAGAAGAAAACAACCATACAGTCTTTCCAG","data_source":"ncbi","molecule_type":"DNA","database":"NCBI","id":"NG_033923","gene_name":"IRGMP","gene_description":"immunity-related GTPase family, M, pseudogene","organism":"Callithrix jacchus","url":"https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/NG_033923","gene_synonyms":null,"gene_type":"other","chromosome":"2","genomic_location":"1-830","function":null,"title":"Callithrix jacchus immunity-related GTPase family, M, pseudogene (IRGMP) on chromosome 2","sequence":"GAACTCCTGACCTCAGGTGATCCACCTGCTTTGGCCTCCCAAAATGCCAGGATTACAGGTATGAGCCACCACGCCCAGCCAGCATTGGGGTATATCGAAGGCAGAGGTCATGAATGTTGAGAGAGCCTCAGCAGATGGGGACTTGCCAGAGGTGGTCTCTGCCATCAAGGAGAGTTTGAAGATAGTGTTCAGGACACCAGTCAACATCGCTATGGCAGGGGACTCTGGCAATAGCATATCCACCTTCATCAGTGCACTTCAAATCGCAGGGCATGAGGCGAAGGCCTCACCTCCTACTGGGCTGGTAAAAGCTACCCAAAGATGTGCCTCCTATTTCTCTTCCCGCTTTCCAAATGTGGTGCTGTGGGATCTGCCTGGAGCAGGGTCTGCCACCAAAACTCTGGAGAACTACCTGATGGAAATGTAGTTCAACCAATATGACTTCATCATGGTTGCATCTGCACAATTCAGCATGAATCATGTGATCCTTGCCAAAACCATTGAGGACATGGGAAAGAAGTTCTACATTGTCTGGACCAAGCTGGACATGGATCTCAGCACAGGTGCCCTCCCAGAAGTGCAGCTACTGTAAATCAGAGAAAATGTCCTGGAAAGTCTCCAGAGGGAGCAGGTATGTGAACTCCCCATATTTATGGCCTCCAGCCTTGAACCTTTATTGCATGACTTCCCAAAGCTTAGAGACACATTGCAAAAGACTCATCCAAATTAGGTGCCATGGCCCTCTTCAAAACCTGTCCCACACCTGTGAGATGATCACGAATGACAAAGCAATCTCCCTGCAGAAGAAAACAACCATACAGTCTTTCCAG","sequence_length":830,"gene_id":"100409682","molecule_type_detail":"genomic region","_search_query":"NG_033923"}
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{"_doc_id":"doc-NG_056118","type":"dna","content":"Title: Homo sapiens major histocompatibility complex, class II, DR beta 8 (pseudogene) (HLA-DRB8) on chromosome 6\nSequence: GCCAGAGCCTAGGTTTACAGAGAAGCAGACAAACAAAACAGCCAAACAAGGAGACTTACTCTGTCTTCATGACTCATTCCCTCTACATTTTTTCTTCTAGTCCATCCTAAGGTGACTGTGTATCCTTTAAAGACCCAGCCCCTGCAGCACCACAACCTCCTGGTCTGCTCTGTGAGTGGTTTCTGTCCAGCCAGCATTGAAGTCAGGTGGTTCCGGAACGGCCAGGAAGAGAAGGCTGGGGTGGTGTCCACAGGCCTGATCCAGAATGGAGACTGGACCTTCCAGACACTGATGATGCTGGAAACAGTTCCTCAGAGTGGAGAGGTTTACACCTGCCAAGTGGAGCATCCAAGCATGATGAGCCCTCTCACGGTGCAATGGAGTTAGCAGCTTTCTGACTTCATAAATTTTTCACCCAGTAAGTACAGGACTGTGCTAATCCCTGAGTGTCAGGTTTCTCCTCTCCCACATCCTATTTTCATTTGCTCCATATTCTCATCTCCATCAGCACAGGTCACTGGGGATAGCCCTGTAATCATTTCTAAAAGCACCTGTACCCCATGGTAAAGCAGTCATGCCTGCCAGGCGGGAGAGGCTGTCTCTCTTTTGAACCTCCCCATGATGGCACAGGTCAGGGTCACCCACTCTCCCTGGCTCCAGGCCCTGCCTCTGGGTCTGAGATTGTATTTCTGCTGCTGTTGCTCTGGGTTGTTTGTTGTGATCTGAGAAGAGGAGAACTGTAGGGGTCTTCCTGGCATGAGGGGAGTCCAATCCCAGCTCTGCCTTTTATTAGCTCTGTCACTCTAGACAAACTACTAAACCTCTTTGAGTCTCAGGATTTCTGTGGATCAGATGTCAAAGTCATGCCTTACATCAAGGCTGTAATATTTGAATGAGTTTGAGGCCTAACCTTGTAACTGTTCAGTGTGATCTGAAAACCTTTTTTCCCCAGAAATAGCTAGTTATTTTAGTTCTTGCAGGGCAGCCTTCTTCCCCATTTTCAAAGCTCTGAATCTCAGTATCTCAATTACAGAGGTTCAATTTGGGATAAAAATCACTAAACCTGGCTTCCACTCTCAGGAGCATGGTCTGAATCTGCACAGAGCAAGATGCTGAGTGGAGTCGGGGGCTTTGTGCTGGGCCTGCTCTTCCTTGGGGCCGGGCTGTTTCTCTACTTCAGGAATCAGAAAGGTGAGGAACCTTTCGTAGCTGGCTCTCTCCATAGACTTTTCTGGAGGAGGAAATATGGCTTTGCAGAGGTTAGTTCTCAGTATATGAGTGGCCCTGGATAAAGCCTTTCTTTCCCAAAACGACCTCCAATGTCCCGCTAATCCAGAAATCATCAGTGCATGGTTACTATGTCAAAGCATAATAGCTTATGGCCTGCAGAGAGAAAAGAAAGGCTAACAAGTAGGGATCCTTTGGTTGGAGATCCTGGAGCAAATTAAGGAAGAGCCACTAAGGTTAATACAATTACACTGGATCCTATGACAGACACTTCACGCTTCAGGGGTCACGTGGTGAGTTTCTGCTCCTCTCTGCCCTGGTTCATGTAAGTTGTGGTGTTAGAGAAATCTCAGGTGGGAGATCTGGGGCTGGGATATTGTGTTGGAGGACAGATTTGCTTCCATATCTTTTTTCTTTTTTCTTTTTTTTGAGACGGAGTCTCGCTCTGTCCCCAGGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCCTTCTCCCGGATTCAAGTGATTCTCCTGCCTCAACCTCCCGAGTAGCTGGGACTATAGGCACCTGCCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAAGATGGTCTCGATCTCTTGACCTTGTGATCCACCCAACTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCACCCGGCCTGCTTCCATATCTTTTAAATGTGTATCTTTTCCCCTTTTTCCCAGGACACTCTGGACTTCAGCCAACAGGTAATACCTTTTCATTCTCTTTTAGAAACAGATTCGCTTTCCTAGAATGATGGTAGAGGTGATAAGGGATGAGACAGAAATAATAGGAAAGACTTTGGATCCAAATTTCTGATCAGGCAATTTACGCCAAAACTCCTCTCTACTTAGAAAAGGCCTGTGCTTGGCCAGGCGCAGTAGCTCATGCCTGTAATCTCAGCACTTTGGGAGGCTGAGGCGGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGACCAACAAGGAGAAACCTTGTCTCTACTAAAAATACAAAAAAAATTAGCCATGCGTGGTGGCGCATGCCTGTAATTCCAGCTACTGAGGAGGCTGAGGTAGGAGAATGGTTTGAAGCTGGGAGGCAGAGGTTGTGGTAAGCGCACCACTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTGAAAAAATGAATAAATAAAAAATAAAAGGCCAGTGCTCTGCAGTAGTATTGGCTCAGGGAGACTTAGCAACTTGTTTTTCTTCTTCCTGTACTGCTTTCATCTGAGTCCCTGAAAGAGGGGGAAAGAAGCTGTTAGTAGAGCCATGTCTGAAAACAACACTCTCCTGTGTCTTCTGCAGGACTCCTGAACTGAAGTGAAGATGACCACATTCAAGGAGGAAACTTCTGCCCCAGCTTTGCAGGAGGAAAAGCTTTTCCGCTTGGCTCTTTTTTTTTTTTTTAGTTTTATTTAT","data_source":"ncbi","molecule_type":"DNA","database":"NCBI","id":"NG_056118","gene_name":"HLA-DRB8","gene_description":"major histocompatibility complex, class II, DR beta 8 (pseudogene)","organism":"Homo sapiens","url":"https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/NG_056118","gene_synonyms":null,"gene_type":"other","chromosome":"6","genomic_location":"1-2737","function":null,"title":"Homo sapiens major histocompatibility complex, class II, DR beta 8 (pseudogene) (HLA-DRB8) on chromosome 6","sequence":"GCCAGAGCCTAGGTTTACAGAGAAGCAGACAAACAAAACAGCCAAACAAGGAGACTTACTCTGTCTTCATGACTCATTCCCTCTACATTTTTTCTTCTAGTCCATCCTAAGGTGACTGTGTATCCTTTAAAGACCCAGCCCCTGCAGCACCACAACCTCCTGGTCTGCTCTGTGAGTGGTTTCTGTCCAGCCAGCATTGAAGTCAGGTGGTTCCGGAACGGCCAGGAAGAGAAGGCTGGGGTGGTGTCCACAGGCCTGATCCAGAATGGAGACTGGACCTTCCAGACACTGATGATGCTGGAAACAGTTCCTCAGAGTGGAGAGGTTTACACCTGCCAAGTGGAGCATCCAAGCATGATGAGCCCTCTCACGGTGCAATGGAGTTAGCAGCTTTCTGACTTCATAAATTTTTCACCCAGTAAGTACAGGACTGTGCTAATCCCTGAGTGTCAGGTTTCTCCTCTCCCACATCCTATTTTCATTTGCTCCATATTCTCATCTCCATCAGCACAGGTCACTGGGGATAGCCCTGTAATCATTTCTAAAAGCACCTGTACCCCATGGTAAAGCAGTCATGCCTGCCAGGCGGGAGAGGCTGTCTCTCTTTTGAACCTCCCCATGATGGCACAGGTCAGGGTCACCCACTCTCCCTGGCTCCAGGCCCTGCCTCTGGGTCTGAGATTGTATTTCTGCTGCTGTTGCTCTGGGTTGTTTGTTGTGATCTGAGAAGAGGAGAACTGTAGGGGTCTTCCTGGCATGAGGGGAGTCCAATCCCAGCTCTGCCTTTTATTAGCTCTGTCACTCTAGACAAACTACTAAACCTCTTTGAGTCTCAGGATTTCTGTGGATCAGATGTCAAAGTCATGCCTTACATCAAGGCTGTAATATTTGAATGAGTTTGAGGCCTAACCTTGTAACTGTTCAGTGTGATCTGAAAACCTTTTTTCCCCAGAAATAGCTAGTTATTTTAGTTCTTGCAGGGCAGCCTTCTTCCCCATTTTCAAAGCTCTGAATCTCAGTATCTCAATTACAGAGGTTCAATTTGGGATAAAAATCACTAAACCTGGCTTCCACTCTCAGGAGCATGGTCTGAATCTGCACAGAGCAAGATGCTGAGTGGAGTCGGGGGCTTTGTGCTGGGCCTGCTCTTCCTTGGGGCCGGGCTGTTTCTCTACTTCAGGAATCAGAAAGGTGAGGAACCTTTCGTAGCTGGCTCTCTCCATAGACTTTTCTGGAGGAGGAAATATGGCTTTGCAGAGGTTAGTTCTCAGTATATGAGTGGCCCTGGATAAAGCCTTTCTTTCCCAAAACGACCTCCAATGTCCCGCTAATCCAGAAATCATCAGTGCATGGTTACTATGTCAAAGCATAATAGCTTATGGCCTGCAGAGAGAAAAGAAAGGCTAACAAGTAGGGATCCTTTGGTTGGAGATCCTGGAGCAAATTAAGGAAGAGCCACTAAGGTTAATACAATTACACTGGATCCTATGACAGACACTTCACGCTTCAGGGGTCACGTGGTGAGTTTCTGCTCCTCTCTGCCCTGGTTCATGTAAGTTGTGGTGTTAGAGAAATCTCAGGTGGGAGATCTGGGGCTGGGATATTGTGTTGGAGGACAGATTTGCTTCCATATCTTTTTTCTTTTTTCTTTTTTTTGAGACGGAGTCTCGCTCTGTCCCCAGGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCCTTCTCCCGGATTCAAGTGATTCTCCTGCCTCAACCTCCCGAGTAGCTGGGACTATAGGCACCTGCCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAAGATGGTCTCGATCTCTTGACCTTGTGATCCACCCAACTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCACCCGGCCTGCTTCCATATCTTTTAAATGTGTATCTTTTCCCCTTTTTCCCAGGACACTCTGGACTTCAGCCAACAGGTAATACCTTTTCATTCTCTTTTAGAAACAGATTCGCTTTCCTAGAATGATGGTAGAGGTGATAAGGGATGAGACAGAAATAATAGGAAAGACTTTGGATCCAAATTTCTGATCAGGCAATTTACGCCAAAACTCCTCTCTACTTAGAAAAGGCCTGTGCTTGGCCAGGCGCAGTAGCTCATGCCTGTAATCTCAGCACTTTGGGAGGCTGAGGCGGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGACCAACAAGGAGAAACCTTGTCTCTACTAAAAATACAAAAAAAATTAGCCATGCGTGGTGGCGCATGCCTGTAATTCCAGCTACTGAGGAGGCTGAGGTAGGAGAATGGTTTGAAGCTGGGAGGCAGAGGTTGTGGTAAGCGCACCACTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTGAAAAAATGAATAAATAAAAAATAAAAGGCCAGTGCTCTGCAGTAGTATTGGCTCAGGGAGACTTAGCAACTTGTTTTTCTTCTTCCTGTACTGCTTTCATCTGAGTCCCTGAAAGAGGGGGAAAGAAGCTGTTAGTAGAGCCATGTCTGAAAACAACACTCTCCTGTGTCTTCTGCAGGACTCCTGAACTGAAGTGAAGATGACCACATTCAAGGAGGAAACTTCTGCCCCAGCTTTGCAGGAGGAAAAGCTTTTCCGCTTGGCTCTTTTTTTTTTTTTTAGTTTTATTTAT","sequence_length":2737,"gene_id":"3130","molecule_type_detail":"genomic region","_search_query":"NG_056118"}

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