{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2011:BC3ZEQRNQG3WYO7UDSRZQ52KVM","short_pith_number":"pith:BC3ZEQRN","canonical_record":{"source":{"id":"1107.2798","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"math.ST","submitted_at":"2011-07-14T12:11:06Z","cross_cats_sorted":["q-bio.QM","stat.TH"],"title_canon_sha256":"ffa0861903c2716dee8918ec30a50316f0ac44671a0d17ad092b0aff106dade2","abstract_canon_sha256":"843d9f3ebba9e9ba9833a9f34835fdd26429c60aba316e10f8074ac9b2e9779f"},"schema_version":"1.0"},"canonical_sha256":"08b792422d81b76c3bf41ca398774aab3134925816136361e1b39e0ec95340eb","source":{"kind":"arxiv","id":"1107.2798","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1107.2798","created_at":"2026-05-18T04:18:14Z"},{"alias_kind":"arxiv_version","alias_value":"1107.2798v1","created_at":"2026-05-18T04:18:14Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1107.2798","created_at":"2026-05-18T04:18:14Z"},{"alias_kind":"pith_short_12","alias_value":"BC3ZEQRNQG3W","created_at":"2026-05-18T12:26:24Z"},{"alias_kind":"pith_short_16","alias_value":"BC3ZEQRNQG3WYO7U","created_at":"2026-05-18T12:26:24Z"},{"alias_kind":"pith_short_8","alias_value":"BC3ZEQRN","created_at":"2026-05-18T12:26:24Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2011:BC3ZEQRNQG3WYO7UDSRZQ52KVM","target":"record","payload":{"canonical_record":{"source":{"id":"1107.2798","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"math.ST","submitted_at":"2011-07-14T12:11:06Z","cross_cats_sorted":["q-bio.QM","stat.TH"],"title_canon_sha256":"ffa0861903c2716dee8918ec30a50316f0ac44671a0d17ad092b0aff106dade2","abstract_canon_sha256":"843d9f3ebba9e9ba9833a9f34835fdd26429c60aba316e10f8074ac9b2e9779f"},"schema_version":"1.0"},"canonical_sha256":"08b792422d81b76c3bf41ca398774aab3134925816136361e1b39e0ec95340eb","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T04:18:14.985859Z","signature_b64":"GQJyojv0+VwGp3zqzsbeD5E4ad8TiftKIsrq9hP7cvWr2NIYAYsAyDZdj5tlIqiwpnofmyoeiIGoB3vAeNeeAg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"08b792422d81b76c3bf41ca398774aab3134925816136361e1b39e0ec95340eb","last_reissued_at":"2026-05-18T04:18:14.985301Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T04:18:14.985301Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1107.2798","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T04:18:14Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"OlnPKFPEMdIjWBrSBVQEPyLOS+zmJ6mzvNWTilC56fXf7N9xgPyVIivnpC35GuhEPsqam3OngrYjtnQW7Ip7Dw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T12:35:16.010540Z"},"content_sha256":"7569ce86ee4cfb9dcd6824b9b2a4d51ecec908560877f2406c15acf6d4fcd631","schema_version":"1.0","event_id":"sha256:7569ce86ee4cfb9dcd6824b9b2a4d51ecec908560877f2406c15acf6d4fcd631"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2011:BC3ZEQRNQG3WYO7UDSRZQ52KVM","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"A context dependent pair hidden Markov model for statistical alignment","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.QM","stat.TH"],"primary_cat":"math.ST","authors_text":"Ana Arribas-Gil, Catherine Matias (SG)","submitted_at":"2011-07-14T12:11:06Z","abstract_excerpt":"This article proposes a novel approach to statistical alignment of nucleotide sequences by introducing a context dependent structure on the substitution process in the underlying evolutionary model. We propose to estimate alignments and context dependent mutation rates relying on the observation of two homologous sequences. The procedure is based on a generalized pair-hidden Markov structure, where conditional on the alignment path, the nucleotide sequences follow a Markov distribution. We use a stochastic approximation expectation maximization (saem) algorithm to give accurate estimators of p"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1107.2798","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T04:18:14Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"+TA7hnVBj9EBHNX7Xw6Pr9vtAS53ytxqaXDK8QlavtPpWQqwlFDmpei3jHJqeHTXazfXwrB+WZZMljDbGsQkAg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T12:35:16.010886Z"},"content_sha256":"7395e1a176dc673a8a11e6d4ab68fc538a5642896c8e5b409b167b31c9978e47","schema_version":"1.0","event_id":"sha256:7395e1a176dc673a8a11e6d4ab68fc538a5642896c8e5b409b167b31c9978e47"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/BC3ZEQRNQG3WYO7UDSRZQ52KVM/bundle.json","state_url":"https://pith.science/pith/BC3ZEQRNQG3WYO7UDSRZQ52KVM/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/BC3ZEQRNQG3WYO7UDSRZQ52KVM/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-05-28T12:35:16Z","links":{"resolver":"https://pith.science/pith/BC3ZEQRNQG3WYO7UDSRZQ52KVM","bundle":"https://pith.science/pith/BC3ZEQRNQG3WYO7UDSRZQ52KVM/bundle.json","state":"https://pith.science/pith/BC3ZEQRNQG3WYO7UDSRZQ52KVM/state.json","well_known_bundle":"https://pith.science/.well-known/pith/BC3ZEQRNQG3WYO7UDSRZQ52KVM/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2011:BC3ZEQRNQG3WYO7UDSRZQ52KVM","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"843d9f3ebba9e9ba9833a9f34835fdd26429c60aba316e10f8074ac9b2e9779f","cross_cats_sorted":["q-bio.QM","stat.TH"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"math.ST","submitted_at":"2011-07-14T12:11:06Z","title_canon_sha256":"ffa0861903c2716dee8918ec30a50316f0ac44671a0d17ad092b0aff106dade2"},"schema_version":"1.0","source":{"id":"1107.2798","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1107.2798","created_at":"2026-05-18T04:18:14Z"},{"alias_kind":"arxiv_version","alias_value":"1107.2798v1","created_at":"2026-05-18T04:18:14Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1107.2798","created_at":"2026-05-18T04:18:14Z"},{"alias_kind":"pith_short_12","alias_value":"BC3ZEQRNQG3W","created_at":"2026-05-18T12:26:24Z"},{"alias_kind":"pith_short_16","alias_value":"BC3ZEQRNQG3WYO7U","created_at":"2026-05-18T12:26:24Z"},{"alias_kind":"pith_short_8","alias_value":"BC3ZEQRN","created_at":"2026-05-18T12:26:24Z"}],"graph_snapshots":[{"event_id":"sha256:7395e1a176dc673a8a11e6d4ab68fc538a5642896c8e5b409b167b31c9978e47","target":"graph","created_at":"2026-05-18T04:18:14Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"paper":{"abstract_excerpt":"This article proposes a novel approach to statistical alignment of nucleotide sequences by introducing a context dependent structure on the substitution process in the underlying evolutionary model. We propose to estimate alignments and context dependent mutation rates relying on the observation of two homologous sequences. The procedure is based on a generalized pair-hidden Markov structure, where conditional on the alignment path, the nucleotide sequences follow a Markov distribution. We use a stochastic approximation expectation maximization (saem) algorithm to give accurate estimators of p","authors_text":"Ana Arribas-Gil, Catherine Matias (SG)","cross_cats":["q-bio.QM","stat.TH"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"math.ST","submitted_at":"2011-07-14T12:11:06Z","title":"A context dependent pair hidden Markov model for statistical alignment"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1107.2798","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:7569ce86ee4cfb9dcd6824b9b2a4d51ecec908560877f2406c15acf6d4fcd631","target":"record","created_at":"2026-05-18T04:18:14Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"843d9f3ebba9e9ba9833a9f34835fdd26429c60aba316e10f8074ac9b2e9779f","cross_cats_sorted":["q-bio.QM","stat.TH"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"math.ST","submitted_at":"2011-07-14T12:11:06Z","title_canon_sha256":"ffa0861903c2716dee8918ec30a50316f0ac44671a0d17ad092b0aff106dade2"},"schema_version":"1.0","source":{"id":"1107.2798","kind":"arxiv","version":1}},"canonical_sha256":"08b792422d81b76c3bf41ca398774aab3134925816136361e1b39e0ec95340eb","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"08b792422d81b76c3bf41ca398774aab3134925816136361e1b39e0ec95340eb","first_computed_at":"2026-05-18T04:18:14.985301Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T04:18:14.985301Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"GQJyojv0+VwGp3zqzsbeD5E4ad8TiftKIsrq9hP7cvWr2NIYAYsAyDZdj5tlIqiwpnofmyoeiIGoB3vAeNeeAg==","signature_status":"signed_v1","signed_at":"2026-05-18T04:18:14.985859Z","signed_message":"canonical_sha256_bytes"},"source_id":"1107.2798","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:7569ce86ee4cfb9dcd6824b9b2a4d51ecec908560877f2406c15acf6d4fcd631","sha256:7395e1a176dc673a8a11e6d4ab68fc538a5642896c8e5b409b167b31c9978e47"],"state_sha256":"4b0d812448fad820435a19cceed7190464db4df24236adb89ea3cf94045d3c61"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"ExfadffOTYXEKmHuQMvt585M69ohRoOiUfVR+SyxmZTbDT/F7/P6xE+P7sY+xl2QI05+faB9LkaG3lKPTMcIBA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-28T12:35:16.012940Z","bundle_sha256":"875357a4f3509ed89b715d214a5b9939ef8e018002c7485c490e12beef22195f"}}