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Old 09-12-2011, 05:29 AM   #1
ketan_bnf
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Location: India

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Default Create one sequence based on overlapping primer sequences in amplicon

Hi all,

Recently we have carried out amplicon sequencing for metagenome. I want to create a single long sequence based on overlapping primers, so i can get whole gene. How can i accomplish this? Is there any softwares for that?

Thanks.
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Old 09-12-2011, 07:53 PM   #2
Kennels
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You could try SSPACE, if you already have a template do the extension on. SSPACE is a scaffolder/contig extender, so you would be using it's extension functionality, and using your primers as 'reads' and amplicon as contig.
However, it takes pair-end reads as input, so you might have to make a dummy read for each primer, though i've never tried this before.
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Old 09-15-2011, 01:33 AM   #3
boetsie
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maybe try this software if you already have a set of sequences;

http://derisilab.ucsf.edu/software/price/index.html
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