Tag Archives: alignment

Quick Carmalign

The first batch of sequencing came into today to verify sequence of Olympia oyster qPCR primers.

1) imported .ab1 files into CLC,

2) trimmed “CARM” sequences

Remove old trimming = Yes
Quality trimming = Yes
Quality limit = 0.05
Ambiguity trimming = Yes
Ambiguity limit = 2
Vector trimming = No
User vector trimming = No

3) aligned to comp7220_c0_seq2



Sequencing – PGS Hi 4 (PGS2/COX2)

Sent plasmid prep to ASU (5uL of plasmid + 1uL of 10uM M13F/R). SJW01 = M13F, SJW02 = M13R.


Sequencing looks great! Definitely have a portion of the second isoform of COX/PGS!! Here’s the result of the consensus BLASTed in GenBank>Nucleotide (others)>blastn:

Top hit in the db is COX1/PGS1, and, clearly, there are differences between the two sequences confirming that we have the second isoform (COX2/PGS2). Will design more RACE primers in hopes of obtaining the full-length cDNA sequence.