“10. The NCBI databases are moving targets…”
(Paper No. 1 at right)
The NCBI databases are constantly being added to, which is a good thing. However, conclusions based on BLAST™ searches might change as new data become available. In this short blog we update our Table 1 (first paper) of Sample 26 matches to human, other primates, Canis (dog, wolf, coyote), Ursidae (bears), and all other categories. Out of the 15 best human and 15 best Ursidae hits by score (17 total sequence ranges), the new polar bear data (in red) improved the previous best Ursidae match 11 times, same four times, not as good as panda 2 times. The overall best matches are still all bears. I look forward to the day when the black bear genome is completely sequenced. My prediction: black bear will be the best match in all cases, near 100%ID. For now the surrogate polar bear in the same Ursus genus will have to do. Sample 26 is a bear (with minor human contamination), as determined experimentally by three independent laboratories (See Sykes and Huggins at right, Cutino: http://www.bf-field-journal.blogspot.com/p/ketchum-dna-study-sample-26.html) and from searching the NCBI databases with the Ketchum sequence - results in the table below.
(Please excuse the overlap on the right.)
| Table 1. S26 Top 15 Human Hits AND Top 15 Ursidae Hits | Revised 10-7-14 | |||||||
| Additions in Red | ||||||||
| S26 vs. | Match(a) | % ID | LEN | MIS | GAP | Start(b) | End(c) | SCORE |
| human-N(1)(d) | BC038508.1 | 93.32 | 2142 | 114 | 13 | 189026 | 191141 | 3136 |
| OP(f)-N: chimpanzee | XM_003951836.1 | 93.18 | 2142 | 117 | 10 | 189026 | 191141 | 3120 |
| dog-N | NM_001097982.2 | 95.36 | 2089 | 72 | 7 | 189026 | 191089 | 3297 |
| polar bear()-RS | NW_007929448.1 | 98.83 | 2139 | 0 | 1 | 189028 | 191141 | 3788 |
| polar bear(1)-TSA | GAJD01008005.1 | 98.69 | 2134 | 0 | 12 | 189028 | 191136 | 3760 |
| AO(g)-N: Pacific walrus(h) | XM_004394587.1 | 96.58 | 2136 | 45 | 12 | 189026 | 191136 | 3515 |
| human-N(2) | NG_012881.1 | 95.85 | 1495 | 33 | 14 | 362696 | 364161 | 2390 |
| OP-G: orangutan | NC_012602.1 | 95.52 | 1497 | 35 | 15 | 362696 | 364161 | 2364 |
| dog-RS | NC_006603.3 | composite | 10 | 10 | 362697 | 364161 | 2595 | |
| polar bear()-RS | NW_007907318.1 | 100 | 1103 | 0 | 0 | 363059 | 364161 | 2037 |
| polar bear()-RS | NW_007907318.1 | 99.19 | 371 | 1 | 2 | 362696 | 363064 | 667 |
| giant panda-G(4) | NW_003217713.1 | 97.32 | 1494 | 9 | 5 | 362698 | 364161 | 2508 |
| AO-N: mouse | AC158579.7 | 92.91 | 1100 | 43 | 17 | 363059 | 364130 | 1567 |
| human-N(3) | NM_001039618.2 | 92.27 | 1695 | 73 | 34 | 1655921 | 1657569 | 2351 |
| OP-N: n. white-cheeked gibbon | XM_003254601.2 | 92.96 | 1690 | 73 | 24 | 1655921 | 1657569 | 2420 |
| dog-RS | NC_006603.3 | 94.89 | 1682 | 35 | 21 | 1655921 | 1657569 | 2582 |
| polar bear()-RS | NW_007907230.1 | 97.86 | 1679 | 2 | 4 | 1655920 | 1657569 | 2870 |
| giant panda(2)-G | NW_003217478.1 | 96.45 | 1688 | 7 | 13 | 1655920 | 1657569 | 2736 |
| AO-N: cattle | BC142239.1 | 92.60 | 1555 | 57 | 31 | 1655921 | 1657446 | 2182 |
| human-N(4) | Z83001.1 | 98.71 | 1239 | 15 | 1 | 690618 | 691855 | 2198 |
| OP-G: chimpanzee | NC_006478.3| | 98.79 | 1239 | 14 | 1 | 690618 | 691855 | 2204 |
| dog-N | AC203200.2 | 99.03 | 1238 | 11 | 1 | 690618 | 691854 | 2218 |
| polar bear()-RS | NW_007907078.1 | 99.92 | 1237 | 1 | 0 | 690618 | 691854 | 2279 |
| giant panda-G(10) | NW_003217489.1 | 99.35 | 1237 | 8 | 0 | 690618 | 691854 | 2241 |
| AO-N: pig | CU462945.6 | 98.45 | 1229 | 17 | 2 | 690624 | 691851 | 2163 |
| human-G+T(5) | NT_009237.18 | 93.90 | 1460 | 67 | 19 | 312074 | 313518 | 2183 |
| OP-N: gorilla | XM_004050754.1 | 94.44 | 1403 | 63 | 14 | 312127 | 313518 | 2145 |
| dog-RS | NC_006603.3 | 94.18 | 1444 | 40 | 13 | 312098 | 313519 | 2161 |
| polar bear ( )-RS | NW_007907318.1 | 99.59 | 1449 | 3 | 2 | 312074 | 313520 | 2639 |
| giant panda-G(3) | NW_003217713.1 | 98.00 | 1453 | 18 | 6 | 312074 | 313519 | 2512 |
| AO-N: Florida manatee | XM_004369676.1 | 92.18 | 1420 | 73 | 25 | 312127 | 313522 | 1973 |
| human-N(7) | NM_001278163.1 | 94.76 | 1354 | 35 | 15 | 759948 | 761288 | 2074 |
| OP-N: n. white-cheeked gibbon | XM_003254384.2 | 95.20 | 1353 | 34 | 12 | 759948 | 761288 | 2109 |
| dog-G | NC_006600.3 | 97.55 | 1349 | 20 | 5 | 759948 | 761288 | 2296 |
| polar bear ( )-RS | NW_007907078.1| | 98.60 | 1359 | 1 | 1 | 759948 | 761288 | 2388 |
| polar bear-N(6)-TSA | GAJD01025080.1 | 98.60 | 1359 | 1 | 5 | 759948 | 761288 | 2388 |
| AO-N: Pacific walrus | XM_004406102.1 | 97.94 | 1357 | 12 | 6 | 759948 | 761288 | 2337 |
| human-G+T(6) | NW_004078072.1 | 92.53 | 1459 | 94 | 7 | 1761457 | 1762900 | 2076 |
| OP-N: chimpanzee | XM_001136982.3 | 92.53 | 1459 | 94 | 7 | 1761457 | 1762900 | 2076 |
| Canis-N: dog | XM_843414.2 | 94.65 | 1459 | 63 | 6 | 1761457 | 1762900 | 2248 |
| polar bear ( )-RS | NW_007907090.1 | 98.9 | 1460 | 1 | 2 | 1761456 | 1762900 | 2593 |
| giant panda-N(5): | XM_002920733.1 | 97.67 | 1460 | 19 | 4 | 1761456 | 1762900 | 2494 |
| AO-N: Pacific walrus | XM_004410744.1 | 95.27 | 1459 | 54 | 4 | 1761457 | 1762900 | 2298 |
| human-N(8) | NM_001039618.2 | 93.39 | 1376 | 54 | 15 | 1657663 | 1659004 | 2002 |
| OP-N: small-eared galago | XM_003780852.1 | 94.43 | 1364 | 48 | 10 | 1657662 | 1659004 | 2073 |
| dog-G | NC_006603.3 | composite | 1657662 | 1659004 | 2336 | |||
| polar bear ( )-RS | NW_007907230.1 | 99.87 | 787 | 1 | 0 | 1658089 | 1658875 | 1448 |
| polar bear ( )-RS | NW_007907230.1 | 99.77 | 429 | 1 | 0 | 1657662 | 1658090 | 787 |
| giant panda-G(7) | XR_097023.1 | incomplete composite | 1657663 | 1658930 | 2312 | |||
| AO-N: star-nosed mole | XM_004683259.1 | 93.51 | 1371 | 47 | 17 | 1657663 | 1659004 | 2001 |
| human-N(9) | NG_012881.1 | 94.27 | 1308 | 63 | 6 | 326857 | 328153 | 1989 |
| OP-G: gorilla | NC_018435.1 | 94.11 | 1308 | 65 | 4 | 326857 | 328153 | 1978 |
| dog-RS | NC_006603.3 | 97.38 | 1300 | 29 | 4 | 326857 | 328153 | 2207 |
| polar bear ( )-RS | NW_007907318.1 | 99.46 | 1299 | 4 | 2 | 326857 | 328153 | 2357 |
| panda-RS(8) | NW_003217713.1 | 98.69 | 1300 | 13 | 3 | 326857 | 328153 | 2303 |
| AO-N: mouse | AC107371.17 | 84.86 | 1268 | 148 | 25 | 326867 | 328112 | 1238 |
| human-N(10) | AC080100.7 | 95.03 | 1268 | 48 | 8 | 855386 | 856643 | 1978 |
| OP-N: n. white-cheeked gibbon | XM_003254447.2 | 95.39 | 1064 | 43 | 3 | 855581 | 856643 | 1688 |
| dog-G | NC_006600.3 | 96.37 | 1267 | 30 | 7 | 855387 | 856643 | 2071 |
| polar Bear-TSA(): | NW_007907185.1 | 99.05 | 1267 | 2 | 2 | 855387 | 856643 | 2265 |
| polar bear ( )-RS | GAJD01033484.1 | 99.05 | 1267 | 2 | 5 | 855387 | 856643 | 2265 |
| AO-N: Pacific walrus | XM_004404764.1 | 97.71 | 1265 | 18 | 6 | 855387 | 856643 | 2165 |
| human-N(11) | AC093262.2 | 98.03 | 1117 | 19 | 2 | 673215 | 674328 | 1938 |
| OP-G: crab-eating macaque | NC_022285.1 | 98.21 | 1118 | 15 | 2 | 673215 | 674327 | 1949 |
| dog-G | NC_006600.3 | 99.1 | 1114 | 10 | 0 | 673215 | 674328 | 2002 |
| polar bear ( )-RS | NW_007907078.1 | 99.91 | 1115 | 0 | 1 | 673215 | 674328 | 2052 |
| giant panda-TSA(15) | NW_003217489.1 | 99.28 | 1114 | 5 | 1 | 673215 | 674328 | 2010 |
| AO-N: pig | CU468610.6 | 98.57 | 1115 | 10 | 4 | 673218 | 674328 | 1965 |
| human-N(12) | NG_027813.1 | 96.28 | 1156 | 42 | 1 | 2258575 | 2259729 | 1895 |
| OP-N: pygmy chimpanzee | DQ977225.1 | 96.37 | 1156 | 41 | 1 | 2258575 | 2259729 | 1901 |
| dog-N | XM_536554.3 | 95.30 | 1149 | 54 | 0 | 2258573 | 2259721 | 1823 |
| polar bear ( )-RS | NW_007907111.1 | 99.65 | 1157 | 4 | 0 | 2258573 | 2259729 | 2115 |
| Ursidae-N(13):giant panda | XM_002927883.1 | 99.65 | 1149 | 4 | 0 | 2258573 | 2259721 | 2100 |
| AO-N: Pacific walrus | XM_004412631.1 | 98.95 | 1147 | 12 | 0 | 2258575 | 2259721 | 2052 |
| human-N(13) | AL122015.17 | 96.75 | 1109 | 36 | 0 | 756650 | 757758 | 1849 |
| OP-N: n. white-cheeked gibbon | XM_003254385.2 | 96.74 | 1104 | 35 | 1 | 756646 | 757748 | 1838 |
| dog-G | NC_006600.3 | 97.66 | 1109 | 26 | 0 | 756650 | 757758 | 1905 |
| polar bear ( )-RS | NW_007907078.1 | 99.73 | 1110 | 3 | 0 | 756650 | 757759 | 2034 |
| giant panda-G | NW_003217489.1 | 98.20 | 1110 | 17 | 1 | 756650 | 757759 | 1936 |
| AO-N: Pacific walrus | XM_004406102.1 | 98.91 | 1099 | 12 | 0 | 756650 | 757748 | 1964 |
| human-N(14) | NG_012881.1 | 95.22 | 1172 | 30 | 11 | 359243 | 360388 | 1831 |
| OP-G: small-eared galago | NW_003852396.1 | 95.4 | 1173 | 27 | 3 | 359243 | 360388 | 1842 |
| dog-G | NC_006603.3 | 97.44 | 1171 | 5 | 1 | 359243 | 360388 | 1973 |
| polar bear ( )-RS | NW_007907318.1 | 97.35 | 1171 | 1 | 3 | 359243 | 360388 | 1964 |
| giant panda-RS | NW_003217713.1 | 97.78 | 1171 | 1 | 1 | 359243 | 360388 | 1995 |
| AO-N: mouse | AC158579.7 | 90.81 | 1175 | 73 | 16 | 359243 | 360388 | 1539 |
| human-N(15) | NM_002233.3 | 94.77 | 1185 | 45 | 12 | 602053 | 603228 | 1829 |
| OP-N: olive baboon | XM_003910099.1 | 95.27 | 1185 | 45 | 8 | 602053 | 603228 | 1868 |
| dog-N | XM_542545.2 | 93.07 | 895 | 56 | 4 | 602341 | 603229 | 1304 |
| polar bear ( )-RS | NW_007907078.1 | 97.96 | 1175 | 1 | 1 | 602054 | 603228 | 2015 |
| giant panda(12)-RS | NW_003218343.1 | 98.99 | 1184 | 3 | 2 | 602054 | 603228 | 2111 |
| AO-N: Pacific walrus | XM_004412889.1 | 97.30 | 1183 | 23 | 3 | 602055 | 603228 | 1999 |
| human-G+T | NW_004078072.1 | 93.87 | 1175 | 65 | 5 | 1835440 | 1836608 | 1764 |
| OP-N: gorilla | XM_004052006.1 | 93.79 | 1175 | 66 | 5 | 1835440 | 1836608 | 1759 |
| dog-N | XM_533970.3 | 92.99 | 1155 | 76 | 4 | 1835459 | 1836608 | 1679 |
| polar bear ( )-RS | NW_007907090.1 | 99.23 | 1174 | 4 | 1 | 1835440 | 1836608 | 2113 |
| polar bear(11)-TSA | GAJD01015683.1 | 99.23 | 1174 | 4 | 3 | 1835440 | 1836608 | 2113 |
| AO: Pacific walrus | XM_004398087.1 | 97.36 | 1174 | 26 | 3 | 1835440 | 1836608 | 1991 |
| human-N | AP000609.5 | 93.29 | 1147 | 62 | 7 | 1508092 | 1509231 | 1677 |
| OP-N: chimpanzee | XM_003808137.1 | 93.29 | 1147 | 60 | 9 | 1508090 | 1509231 | 1676 |
| dog-G | NC_006603.3 | 95.45 | 1144 | 30 | 8 | 1508103 | 1509231 | 1805 |
| polar bear ( )-RS | NW_007907285.1 | 98.96 | 1151 | 0 | 2 | 1508093 | 1509231 | 2049 |
| polar bear(14)-TSA | GAJD01035976.1 | 98.96 | 1151 | 0 | 2 | 1508093 | 1509231 | 2049 |
| AO-N: domestic ferret | XM_004795929.1 | 96.04 | 1161 | 16 | 11 | 1508093 | 1509231 | 1862 |
| (a) NCBI accession number. | ||||||||
| (b) First position of matching query (S26) sequence range. | ||||||||
| (c) Final position of matching query (S26) sequence range. | ||||||||
| (d) "N" indicates Nucleotide Database. Relative score (1-15) in parentheses. | ||||||||
| (e) "G + T" indicates human Genomic plus Transcription Database. | ||||||||
| "G" indicates Genomic Reference Database | ||||||||
| "TSA" indicates Transcriptome Shotgun Assembly Database | ||||||||
| "RS" indicates Reference Sequence Database. | ||||||||
| (f) OP = Other Primates (ex Homo sapiens) | ||||||||
| (g) AO = All Other (ex primates, ex Canis, ex Ursidae) | ||||||||
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