Referencing pAMP sequence in BLAST - (Aug/02/2013 )
I need your help. This may be an elementary BLAST question that may have been covered, but I searched here and could not find it.
I took the pAMP sequence from the CSH: DNA Learning Center: http://www.dnalc.org/resources/plasmids.html
and plugged it into BLAST http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch
The results do not match the coverage for pAMP, I'm getting results for pUC cloning vectors.
Am I doing something incorrect?
I think what you got is right. Probably, according to this site: bhhs.bhusd.org/ourpages/auto/2012/1/.../Amgen%20lab%20handout.doc
The plasmids, pAMP and pKAN, were engineered by the DNA Learning Center at Cold Spring Harbor Laboratory. The pAMP plasmid was engineered from the pUC19 plasmid which contains ampr and a 1904 bp restriction fragment cut from 8 DNA.
Actually you can blast again the vector database http://www.ebi.ac.uk/Tools/sss/ncbiblast/vectors.html
I thought that because of the prevelant use of these plasmids (pAMP and pKAN), their entire sequence would register in BLAST.
Thank you Mod! This is helpful.