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Sunday, November 30, 2014

Table 1 Updated: The Ketchum Sample 26 nDNA

 

“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)BC038508.193.322142114131890261911413136
OP(f)-N: chimpanzeeXM_003951836.193.182142117101890261911413120
dog-NNM_001097982.295.3620897271890261910893297
polar bear()-RSNW_007929448.198.832139011890281911413788
polar bear(1)-TSAGAJD01008005.198.6921340121890281911363760
AO(g)-N: Pacific walrus(h)XM_004394587.196.58213645121890261911363515









human-N(2)NG_012881.195.85149533143626963641612390
OP-G: orangutanNC_012602.195.52149735153626963641612364
dog-RSNC_006603.3composite10103626973641612595
polar bear()-RSNW_007907318.11001103003630593641612037
polar bear()-RSNW_007907318.199.1937112362696363064667
giant panda-G(4)NW_003217713.197.321494953626983641612508
AO-N: mouse AC158579.792.91110043173630593641301567









human-N(3)NM_001039618.292.2716957334165592116575692351
OP-N: n. white-cheeked gibbonXM_003254601.292.9616907324165592116575692420
dog-RSNC_006603.394.8916823521165592116575692582
polar bear()-RSNW_007907230.197.86167924165592016575692870
giant panda(2)-GNW_003217478.196.451688713165592016575692736
AO-N: cattleBC142239.192.6015555731165592116574462182









human-N(4)Z83001.198.7112391516906186918552198
OP-G: chimpanzeeNC_006478.3|98.7912391416906186918552204
dog-NAC203200.299.0312381116906186918542218
polar bear()-RSNW_007907078.199.921237106906186918542279
giant panda-G(10)NW_003217489.199.351237806906186918542241
AO-N: pigCU462945.698.4512291726906246918512163









human-G+T(5)NT_009237.1893.90146067193120743135182183
OP-N: gorillaXM_004050754.194.44140363143121273135182145
dog-RSNC_006603.394.18144440133120983135192161
polar bear ( )-RSNW_007907318.199.591449323120743135202639
giant panda-G(3)NW_003217713.198.0014531863120743135192512
AO-N: Florida manateeXM_004369676.192.18142073253121273135221973









human-N(7)NM_001278163.194.76135435157599487612882074
OP-N: n. white-cheeked gibbonXM_003254384.295.20135334127599487612882109
dog-GNC_006600.397.5513492057599487612882296
polar bear ( )-RSNW_007907078.1|98.601359117599487612882388
polar bear-N(6)-TSAGAJD01025080.198.601359157599487612882388
AO-N: Pacific walrusXM_004406102.197.9413571267599487612882337









human-G+T(6)NW_004078072.192.531459947176145717629002076
OP-N: chimpanzeeXM_001136982.392.531459947176145717629002076
Canis-N: dogXM_843414.294.651459636176145717629002248
polar bear ( )-RSNW_007907090.198.9146012176145617629002593
giant panda-N(5): XM_002920733.197.671460194176145617629002494
AO-N: Pacific walrusXM_004410744.195.271459544176145717629002298









human-N(8)NM_001039618.293.3913765415165766316590042002
OP-N: small-eared galagoXM_003780852.194.4313644810165766216590042073
dog-GNC_006603.3composite

165766216590042336
polar bear ( )-RSNW_007907230.199.8778710165808916588751448
polar bear ( )-RSNW_007907230.199.774291016576621658090787
giant panda-G(7)XR_097023.1incomplete composite
165766316589302312
AO-N: star-nosed mole XM_004683259.193.5113714717165766316590042001









human-N(9)NG_012881.194.2713086363268573281531989
OP-G: gorillaNC_018435.194.1113086543268573281531978
dog-RSNC_006603.397.3813002943268573281532207
polar bear ( )-RSNW_007907318.199.461299423268573281532357
panda-RS(8)NW_003217713.198.6913001333268573281532303
AO-N: mouseAC107371.1784.861268148253268673281121238









human-N(10)AC080100.795.0312684888553868566431978
OP-N: n. white-cheeked gibbonXM_003254447.295.3910644338555818566431688
dog-GNC_006600.396.3712673078553878566432071
polar Bear-TSA(): NW_007907185.199.051267228553878566432265
polar bear ( )-RSGAJD01033484.199.051267258553878566432265
AO-N: Pacific walrusXM_004404764.197.7112651868553878566432165









human-N(11)AC093262.298.0311171926732156743281938
OP-G: crab-eating macaqueNC_022285.198.2111181526732156743271949
dog-GNC_006600.399.111141006732156743282002
polar bear ( )-RSNW_007907078.199.911115016732156743282052
giant panda-TSA(15)NW_003217489.199.281114516732156743282010
AO-N: pigCU468610.698.5711151046732186743281965









human-N(12)NG_027813.196.281156421225857522597291895
OP-N: pygmy chimpanzeeDQ977225.196.371156411225857522597291901
dog-NXM_536554.395.301149540225857322597211823
polar bear ( )-RSNW_007907111.199.65115740225857322597292115
Ursidae-N(13):giant  pandaXM_002927883.199.65114940225857322597212100
AO-N: Pacific walrusXM_004412631.198.951147120225857522597212052









human-N(13)AL122015.1796.7511093607566507577581849
OP-N: n. white-cheeked gibbonXM_003254385.296.7411043517566467577481838
dog-GNC_006600.397.6611092607566507577581905
polar bear ( )-RSNW_007907078.199.731110307566507577592034
giant panda-GNW_003217489.198.2011101717566507577591936
AO-N:  Pacific walrusXM_004406102.198.9110991207566507577481964









human-N(14)NG_012881.195.22117230113592433603881831
OP-G: small-eared galagoNW_003852396.195.411732733592433603881842
dog-GNC_006603.397.441171513592433603881973
polar bear ( )-RSNW_007907318.197.35117113359243360388     1964
giant panda-RSNW_003217713.197.781171113592433603881995
AO-N: mouseAC158579.790.81117573163592433603881539









human-N(15)NM_002233.394.77118545126020536032281829
OP-N: olive baboonXM_003910099.195.2711854586020536032281868
dog-NXM_542545.293.078955646023416032291304
polar bear ( )-RSNW_007907078.197.96117511602054603228     2015
giant panda(12)-RSNW_003218343.198.991184326020546032282111
AO-N: Pacific walrus XM_004412889.197.3011832336020556032281999









human-G+TNW_004078072.193.871175655183544018366081764
OP-N: gorillaXM_004052006.193.791175665183544018366081759
dog-NXM_533970.392.991155764183545918366081679
polar bear ( )-RSNW_007907090.199.23117441183544018366082113
polar bear(11)-TSAGAJD01015683.199.23117443183544018366082113
AO: Pacific walrusXM_004398087.197.361174263183544018366081991









human-NAP000609.593.291147627150809215092311677
OP-N: chimpanzeeXM_003808137.193.291147609150809015092311676
dog-GNC_006603.395.451144308150810315092311805
polar bear ( )-RSNW_007907285.198.96115102150809315092312049
polar bear(14)-TSAGAJD01035976.198.96115102150809315092312049
AO-N: domestic ferretXM_004795929.196.0411611611150809315092311862








(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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