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Calling start in FC phage Phrampa
| Link to this post | posted yesterday, 20:17 | |
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Hi all, Our class is looking at Gene 1 (stop 685), which is called by glimmer and genemark (Both), the gene is long enough (120 nt = 40aa), has good coding potential (Yes), has SYNTENY (Yes with FC phages MIMI, TALIA, and ATUIN), is the only gene in the region (Yes), and has a function predicted, (Hypothetical Protein). We need help choosing a start. Both starts 1 and 10 are called by Glimmer and GeneMark. In STARTERATOR, start 1 has two MA's while start 10 has six MA's. Start 1 has lower RBS scores (Z-score of 1.399 and a final score of -6.961), and start 10 has a z-score of 2.024 and a final score of -4.608. Start 1 also has the longest open reading frame. Start 1 gives us 1:1 matches to the highest GenBank hit, while Start 10 gives us 1:1 matches to the second and third GenBank hits. Basically, the highest RBS scores go with start 10, but the longest open reading frame and the top hits go with start 1. Which would be a better start? Thanks! |
| Link to this post | posted today, 01:05 | |
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HI Brian, When I look at the Starterator report, I see one common start for every phage listed - it is technically threaded through the starts listed as 9, 10 and 11. Which is the start that corresponds to bp 110. Remember that starterator is a clustal alignment and as the sequence diverges, small discrepancies at the nucleotide level can be present. I would call 110 as the start. debbie |