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Who could tell me how to do?

Everything on bioinformatics, the science of information technology as applied to biological research.

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Who could tell me how to do?

Postby cnstr14 » Thu Jun 24, 2010 8:13 am

I have downloaded 120 sequences from Genbank for designing primers. However how can I import the referred sequences' Genbank IDs(not including sequences) into my article references section with a simple approach, Thanks.
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Postby JackBean » Thu Jun 24, 2010 12:25 pm

you need to parse only the lines with > in the beginning.
http://www.biolib.cz/en/main/

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Re:

Postby cnstr14 » Thu Jun 24, 2010 1:50 pm

JackBean wrote:you need to parse only the lines with > in the beginning.


Do you mean add ">" at the begining of the each sequence and then import the FASTA format sequences into a soft for further analysis ? But actually I just only need to import the sequences' Genbank id, not including the sequences, into my MS WORD article.
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Postby JackBean » Mon Jul 05, 2010 10:54 am

well, the FASTA format looks like:

>ID_you're_looking_for|stuff you probably don't need|more stuff|and yet other
HEREISYOURSEQUENCEYOU'RENOTINTERESTEDINMOSTLY60OR100LETTE
RSPERLINE;)

so, you need, to pick only the lines starting with ">", so like:
>ID_you're_looking_for|stuff you probably don't need|more stuff|and yet other
http://www.biolib.cz/en/main/

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Postby fcs » Wed Aug 11, 2010 3:49 am

To clean up the sequence information, you can run a "find and replace" with nothing with this regular expression:

^\w+$

Make sure you copy the original file because this will remove all sequence information so that all you are left with are your headers.
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