Skip to content

Instantly share code, notes, and snippets.

@rdmpage

rdmpage/primers.txt

Last active May 17, 2018 10:10
Show Gist options
  • Star 1 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save rdmpage/4f2545eeea4756565925fb4307d9af6b to your computer and use it in GitHub Desktop.
Save rdmpage/4f2545eeea4756565925fb4307d9af6b to your computer and use it in GitHub Desktop.
Download ZIP
COI DNA barcode primer locations
Raw
primers.txt
Reference COI is NC_003128 Buteo buteo COI
TZBRD035-15.COI-5P [648bp] ctgatctttggtgnatgagcaggcatagccggcacagcacttagcctactaatccgcgcagaactaggacagccaggaacactattgggagacgaccaaatctacaatgtaatcgtaacagcccacgctttcgtcataatcttcttcatagtcatacctattatgatcggaggcttcggaaactgactggttccactcataattggcgccccagacatagcattcccccgcataaataatatgagcttctgactcctcccaccttcttttctcctcctactagcctcctctacagtagaagccggggctggcactggatgaactgtttatccacccctagccggtaatcttgcccacgcgggcgcatcagtagacctggctattttttcccttcacttggcaggcgtgtcgtccatcttaggagctattaactttatcaccacaattattaacataaagccccctgcactatcacaatatcaaacacccctcttcgtatgatccgtcctcattactgctatcctcttactactatccctgccagtcctagccgccgggattacaatactcctcaccgatcgcaacctcaacactacattctttgaccctgcaggaggaggagacccaatcctgtatcaacacctattc
TZBRD019-15.COI-5P tcttcggcgcctgagctggtatagtcggcaccgccctcagcttactcatccgtgcagaactcggccaacccggcacactcctaggtgacgaccaaatttataacgtaatcgttaccgcacatgccttcgtaataatcttcttcatagttataccaatcatgatcggaggattcggaaactgacttgttccactcataattggcgctcccgacatagcctttccacgcataaacaacataagcttctgactactccccccatccttcctcctcctactagcttcctcaacagtagaagcaggagccggtactggatgaactgtctatcctcccttagctggcaacatagcccatgccggagcttcagtagacctagccatcttctctctacacttagccggagtttcatccattctaggggcgatcaacttcatcacaaccgccattaatataaaacccccagcactctcccagtaccaaacacccctgtttgtatgatctgtactcatcactgccgtccttctactactctcactcccagtcctagccgctggcatcactatactacttacagaccgaaacctaaacacaacattctttgaccctgccggcggaggcgatcccatcctctaccaacatctcttc
SYROC231-15.COI gacactttatttcatttttggagcttgagcaggaatagtgggaacatctttaagaattttaattcgaacagaattaggtcatccaggagctttaattggtgatgatcaaatttataatgtaattgtaacagctcatgcttttgtaataattttttttatagtaatacctattataattggaggtttcggaaactgattagttcctttaatattaggagctcctgatatagcttttcctcgaataaataatataagtttttgaatacttcccccatctcttactcttcttcttataagaagtatagtagaaaatggagctggaactggctgaaccgtttaccctcccctttcttctactattgctcatagaggagcttcagttgatttagctattttttctcttcatcttgctggaatttcttcaattttaggagcagtaaattttattactacagtaattaatatacgaagctctggaattttatttgatcgaatacctttatttgtctgatcagtattaattactgctattcttttattattatctcttccagttttagcaggagcaattactatattattaactgatcgaaatttaaatacatccttttttgatcctgcaggtggaggtgatcctattttatatcaacacttattt
FARAN267-14.COI-5P (fish) cctttatctagtatttggtgcctgagccggaatagtaggcacagctctaagcctcctcattcgagcggagctaagccaacccggcgccctcctgggagacgaccaaatttataatgtccttgttacagcgcatgcgttcgtaataatcttctttatagtaataccaattatgatcgggggttttggaaactgacttgtacccttgataatcggggccccggacatagcattcccccggataaacaacatgagcttttgactccttcccccatcttttctcctcctccttgcctcttcgggggtggaggcgggcgctggaacggggtgaacagtttacccccctctctcaggtaacttagcccacgcaggggcctccgttgatttaacaatcttttccctccacctagcaggaatttcttcgatcctcggagcaattaatttcattacaaccatcatcaacatgaaaccccctgcgatctctcagtaccagacacccctcttcgtctggtccgtacttgtcacggcggtcctgctcctcctctctcttcccgtcctcgcagccggtatcactatgctcctgacagatcgtaacctaaacaccaccttcttcgaccccgccgggggaggagacccaatcctttaccaacacctg
gtgacatttatcaatcgatgattattctcaaccaatcacaaagacatcggcaccctatacctaatcttcggtgcctgagccggtatagtcggcaccgccctcagcctacttattcgtgcagaactcggccaaccaggcacactcctaggtgacgaccagatctacaacgtaatcgttaccgcacatgccttcgtaataattttctttatagttataccaattatgatcggaggcttcggaaactgacttgttccactcataatcggcgcccccgatatagccttcccacgcataaacaacataagcttctgactacttcctccatcctttctcctcctcctagcctcctcaacagtagaagcaggagccggcactggatgaactgtctatcccccactagctggcaacatagcccatgccggagcttcagtagacctagccatcttctccctccacttagccggagtctcgtccattctaggagcaatcaactttatcacaaccgccatcaacataaagcccccagccctctcccagtaccaaacacccctattcgtatgatctgtcctcattaccgctgtccttctactactctcactcccagtcctagccgccggcattaccatactacttacagaccgaaacctaaacacaacattctttgaccccgccggcggaggtgatcctatcctataccaacatctcttttgattcttcggacacccagaagtttacatcctaatcctacccggcttcggaattatctcccacgtagtaacatactatgcaggcaaaaaagaaccattcggttacataggaatagtatgagccatactatcaatcggattcctagggttcatcgtatgagctcatcacatatttacagtagggatagacgtggacacccgagcatacttcacatctgctactataatcattgctatcccaactggtattaaagtcttcagctgactagcaacgctccacggaggaactatcaaatgagaccctccaatattatgagcccttggcttcatcttcctctttaccatcggaggcctaacaggaatcgtcctagctaactcctcactagacatcgctctacacgacgcatactatgtagttgcccacttccactacgtcctctcaataggagctgtctttgccattctagcaggattcacccactgattccctctattaactggattcaccctccaccccacatgagctaaagcccacttcggggttatattcacaggagtaaatctaactttcttcccacaacacttcctaggcctcgccggaatacctcgacgatattccgactacccagacgcctataccctatgaaacaccctatcctctatcggctcactaatctcaataacagccgtaatcatactaatattcatcatctgagaagcctttgcctcaaaacgaaaaatcctacaaccagaactaaccacaaccaatgtcgaatgaatccacggctgcccacctccataccacacctttgaagaaccagcctttgttcaagtacaagaaagg
|| || |||||||| || || || || || ||||||||| | || |||||| | || || |||||||||||||||||
minbarF1 tccactaatcacaargatattggtac gctcatgccttcattatgattttc minibarR1 reverse complement caggatttggaattatctcccacgt BirdR1
| | | | | |
1 54 61 180 708 748
BirdF1 ttctccaaccacaaagacattggcac
minbarF1 tccactaatcacaargatattggtac
minbarR1 gaaaatcataatgaaggcatgagc
A universal DNA mini-barcode for biodiversity analysis
http://dx.doi.org/10.1186/1471-2164-9-214
Applicability of DNA barcoding to museum specimens of birds from the Democratic Republic of the Congo
http://biostor.org/reference/137082
Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., & Francis, C. M. (2004, September 28). Identification of Birds through DNA Barcodes. (Charles Godfray, Ed.)PLoS Biology. Public Library of Science (PLoS). http://doi.org/10.1371/journal.pbio.0020312
@rdmpage
Copy link
Author

rdmpage commented May 10, 2016

44835517 500 500

@rdmpage
Copy link
Author

rdmpage commented May 17, 2018

NGS barcodes used in Rudolf Meier's lab, e.g. Meier, R., Wong, W., Srivathsan, A., & Foo, M. (2015). $1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples. Cladistics, 32(1), 100–110. doi:10.1111/cla.12115

Below is traditional COI barcode from LC096192 and NGS barcode KP461672 for same species, with the m1CO1intF primer (forward). Bird COI sequence and mini barcode primer from above is shown for comparison (insect sequences are aligned with bird sequence to make coordinates compatible).

Tanytarsus oscillans $1 barcode NGS
LC096192.1                                         aacattatattttatttttggagcctgatctggaatagtagggacttctttaagtatactaatccgtgcagaattaggacaccccggaacatttatcggtgatgaccaaatttataatgtaattgttacagcccacgcttttattataattttttttatagttatgcctattttaattggaggatttggaaattgacttcttcctttaatattaggggccccagatatagccttccctcgaataaataatataagtttttgacttttaccaccctctcttacacttcttctttctagttcaattgtagaaaatggagccggaacaggatgaacagtttatcctcccctatctgctagaattgctcacagaggggcttctgttgatttagctattttttctcttcatcttgcagggatttcttctattttaggatctgtaaattttattactactgctattaatatacgagcaaatggaattacccttgatcgcatacccttatttgtttgatcagttgtaattacaactgttcttcttcttctttcccttccggttcttgctggtgcaattactatacttttaacagatcgaaatttaaatacttcattttttgatccagcaggaggaggagatcctattctttatcaacacttattt
KP461672                                                                                                                                                                                                                                                                                                                                                                                                    cctatctgctagaattgctcatagtggagcctctgttgatttagctattttttctcttcaccttgcaggaatttcttccattttaggttcagtaaattttattactacagctatcaatatacgagcaaatggaattacacttgaccgaatacctttatttgtttgatccgttgtaattacaactgttctccttcttctttcccttccagttctagctggtgcaattactatacttttaacagaccgaaatttaaacacatcattttttgacccggcaggaggaggggaccctatcctctatcaacatttattt
                                                                                                                                                                                                                                                                                                                                                                                  || || || ||||| || || || ||
                                                                                                                                                                                                                                                                                                                                                                  m1CO1intF       GGWACWGGWTGAACWGTWTAYCCYCC                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                  |                                    
                                                                                                                                                                                                                                                                                                                                                                                371                                     
gtgacatttatcaatcgatgattattctcaaccaatcacaaagacatcggcaccctatacctaatcttcggtgcctgagccggtatagtcggcaccgccctcagcctacttattcgtgcagaactcggccaaccaggcacactcctaggtgacgaccagatctacaacgtaatcgttaccgcacatgccttcgtaataattttctttatagttataccaattatgatcggaggcttcggaaactgacttgttccactcataatcggcgcccccgatatagccttcccacgcataaacaacataagcttctgactacttcctccatcctttctcctcctcctagcctcctcaacagtagaagcaggagccggcactggatgaactgtctatcccccactagctggcaacatagcccatgccggagcttcagtagacctagccatcttctccctccacttagccggagtctcgtccattctaggagcaatcaactttatcacaaccgccatcaacataaagcccccagccctctcccagtaccaaacacccctattcgtatgatctgtcctcattaccgctgtccttctactactctcactcccagtcctagccgccggcattaccatactacttacagaccgaaacctaaacacaacattctttgaccccgccggcggaggtgatcctatcctataccaacatctcttttgattcttcggacacccagaagtttacatcctaatcctacccggcttcggaattatctcccacgtagtaacatactatgcaggcaaaaaagaaccattcggttacataggaatagtatgagccatactatcaatcggattcctagggttcatcgtatgagctcatcacatatttacagtagggatagacgtggacacccgagcatacttcacatctgctactataatcattgctatcccaactggtattaaagtcttcagctgactagcaacgctccacggaggaactatcaaatgagaccctccaatattatgagcccttggcttcatcttcctctttaccatcggaggcctaacaggaatcgtcctagctaactcctcactagacatcgctctacacgacgcatactatgtagttgcccacttccactacgtcctctcaataggagctgtctttgccattctagcaggattcacccactgattccctctattaactggattcaccctccaccccacatgagctaaagcccacttcggggttatattcacaggagtaaatctaactttcttcccacaacacttcctaggcctcgccggaatacctcgacgatattccgactacccagacgcctataccctatgaaacaccctatcctctatcggctcactaatctcaataacagccgtaatcatactaatattcatcatctgagaagcctttgcctcaaaacgaaaaatcctacaaccagaactaaccacaaccaatgtcgaatgaatccacggctgcccacctccataccacacctttgaagaaccagcctttgttcaagtacaagaaagg
                           || || |||||||| || || || ||                                                                                                                               || ||||||||| | || ||||||                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | || || |||||||||||||||||
              minbarF1     tccactaatcacaargatattggtac                                                                                                                               gctcatgccttcattatgattttc minibarR1 reverse complement                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   caggatttggaattatctcccacgt BirdR1

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment