Is there an easy way to unify sequences of COI-5P from the two database BOLB and GenBank (NCBI)?

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Abhijeet Singh

Emanuele Berrilli

Better to use single and specific database
In case there is no such possibility, download Everything you want and then remove the duplicates. If you are command line familier, you can use biopython script named "Sequence cleaner" OR very easy to do it in Aliview.

Zhi-Teng Chen

I dont know how you interpreted from the above question and what are you suggesting. I dont Think it is what he want to do.

Nikolaus Szucsich

Dear Emanuele

Depends of what you downloaded

If you download a "combined" file from your search in BOLD then the GenBank Accession number is included and you can do it bioinformatically quite easy (given that you have likewise the same information from GenBank).

It is just that you will have to do some cleaning before maybe.

If you download just the sequencefiles as Fasta the Genbanknumbers are likewise included in the names line

e.g.

KJ124849 in

>GBDCU1042-14|Culiseta longiareolata|COI-5P|KJ124849

TACATTATATTTTATTTTTGGAGCTTGAGCTGGAATAGTAGGGACTTCATTAAGTCTTCTTATTCGAGCAGAATTAAGACACCCAGGAATATTTATTGGGAATGATCAAATTTATAATGTAATTGTAACTGCTCATGCATTTATTATAATTTTTTTCATAGTAATACCTATTATAATTGGAGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTTCCACGAATAAATAATATAAGTTTTTGAATATTACCTCCTTCATTAACACTACTACTTTCTAGAAGTATAGTTGAAAATGGATCAGGAACTGGATGAACAGTTTATCCCCCACTTTCTTCAGGAACAGCTCATGCTGGAGCTTCTGTTGATCTAACAATTTTTTCATTACATTTAGCAGGAATTTCTTCAATTTTAGGAGCTGTAAATTTTATTACTACAGTAATTAATATACGATCAGCAGGAATTTCTCTAGATCGTATACCCTTATTTGTTTGATCAGTAGTGATTACTGCAGTTCTTTTACTTTTATCCTTACCAGTTTTAGCCGGAGCTATTACTATATTATTAACAGATCGAAATTTAAATACATCATTCTTTGACCCTATTGGAGGAGGAGACCCAATTCTTTATCAACATTTAT

All the best

Nikola

HI Abhijeet Singh, thanks a lot for the information. I resolved using vsearch program. I did a single fasta file from BOLD and GeneBank and than I dereplicate the sequences with vsearch command --derep_fulllenght. Do you know this progrma? I'll try also with Aliview.

Emanuele

Emanuele Berrilli Yes, vsearch is of course an option and good option to serve your purpose. If you have a large data set, better to use vsearch.

You can likewise use OpenRefine (http://openrefine.org/) for such purposes.