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Old 11-16-2011, 12:21 AM   #1
-yl-
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Default Align primer against NGS contigs?

i got my NGS data in contigs. i have few sets of primer that amplify certain gene. i would like to align the primer to the contigs to get the DNA sequence of the gene. is there any software can do so?
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Old 11-16-2011, 02:09 AM   #2
maasha
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In Biopieces (www.biopieces.org) there is pcr_seq:

http://code.google.com/p/biopieces/wiki/pcr_seq
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Old 11-16-2011, 05:16 AM   #3
lh3
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most short read mapper will do that accurately and efficiently
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Old 11-20-2011, 11:01 PM   #4
James Hane
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http://www.ncbi.nlm.nih.gov/projects/e-pcr/
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