Talk:20.109(S14):Diagnostic primer design (Day2): Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 4: | Line 4: | ||
Red Team - sensitivity | Red Team - sensitivity | ||
Green Team - sensitivty | Green Team - sensitivty | ||
===Sensitivity=== | |||
{| border="1" | |||
|Team color | |||
|Forward (F) primer | |||
|Reverse (R) primer | |||
|Target site (e.g. bp 60), F | |||
|Target side (e.g., bp 300), R | |||
|Is bp # for VC or EH? Which gene? | |||
|- | |||
| Grey (Platinum) :) | |||
| CAT GCT TGC CAA CAC AG<br>Agi: PT so unchanged | |||
| GAA TGG TCT GGT TGC TTC<br>Agi: PT so unchanged | |||
| bp 9 | |||
| bp 251 | |||
| E. Hellem: polar tube protein gene | |||
|- | |||
|Green | |||
|AGG TTG ATT CTG CCT GAC<br>Agi: fine | |||
|CGG AAC CAA ACC CTG AT<br>Agi: '''C''' CGG '''T'''AC '''A'''AA ACC CT'''A''' AT<br>new G/C = 44.4%, new Tm = 55.8<br>added 1 extra base to increase Tm | |||
|bp 5 | |||
|bp 236 | |||
|VC: SSU rRNA | |||
|- | |||
|Pink | |||
|ttctgcctgacgtagatg<br>Agi: fine | |||
|cctctccggaaccaaac<br>Agi: CCT CTC CGG '''T'''AC '''A'''AA AC <br>new G/C = 52.9%, new Tm = 55.6 | |||
|bp 12 | |||
|bp 226 | |||
|VC | |||
|- | |||
|Yellow | |||
|CTGACGTGGATGCTATTC<br>Agi: '''c''' ctg acg t'''a'''g atg cta '''g'''tc<br>new G/C = 50%, new Tm = 56.4 - oops, 55.1<br>added one more "c" at 5' for Tm = 57.7 | |||
|CCGTCAACCGTCACTGTC<br>Agi: fine | |||
|bp 18 | |||
|bp 199 | |||
|VC small subunit ribosomal RNA gene | |||
|- | |||
|} | |||
<br style="clear:both;"/> | |||
===Specificity=== | |||
{| border="1" | |||
|Team Color | |||
|Forward primer | |||
|Reverse primer | |||
|Target site (e.g. bp 60), F | |||
|Target side (e.g., bp 300), R | |||
|Is bp # for VC or EH? Which gene? | |||
|- | |||
| Purple | |||
|5' GCG ATG ATT TAG TCT GGC 3'<br>Agi: fine | |||
|5’ CAA TTT CCA ACG ACC ATG C 3’<br>Agi: fine | |||
| bp 93, F | |||
| bp 879, R | |||
|VC, SSU rRNA | |||
|- | |||
|Red | |||
|GGT TGA TTC TGC CTG ACG TGG<br>Agi:fine | |||
|CCT TCG TCC TTC ATC ACC ACA A<br>Agi: CCT TCG TCC TT'''G''' ATC ACC '''GA'''A '''T''' (yours doesn't match ''any'' known sequence in last 4 bp -- do I have right region?)<br>new G/C = 50%, new Tm = 63.5 | |||
|bp 6, F | |||
|bp 588, R | |||
|VC, SSU RNA | |||
|- | |||
|Orange | |||
|5'cgt agt cat aga agg gca aag ag3'<br>Agi: fine | |||
|5' ctc tct ctc tac ctg cta ttg ta 3'<br>Agi: fine | |||
|441 | |||
|1005 | |||
|V. corneae TV4/TV5 SSU rRNA | |||
|- | |||
|Blue | |||
|CCGCAATCAGGGACGAA<br>Agi: fine | |||
|GTCAACGTCACTGTCTTGG<br>Agi: GTC AAC '''C''' GTC ACT GTC TTG G (insertion) <br>new G/C = 55%, new Tm = 61.8 | |||
|60 | |||
|195 | |||
|V. corneae TV4/TV5 SSU rRNA | |||
|- | |||
|} | |||
<br style="clear:both;"/> | |||
Revision as of 12:14, 11 February 2014
Yellow team - selectivity! Blue team-selectivity Orange team - selectivity! Red Team - sensitivity Green Team - sensitivty
Sensitivity
| Team color | Forward (F) primer | Reverse (R) primer | Target site (e.g. bp 60), F | Target side (e.g., bp 300), R | Is bp # for VC or EH? Which gene? |
| Grey (Platinum) :) | CAT GCT TGC CAA CAC AG Agi: PT so unchanged |
GAA TGG TCT GGT TGC TTC Agi: PT so unchanged |
bp 9 | bp 251 | E. Hellem: polar tube protein gene |
| Green | AGG TTG ATT CTG CCT GAC Agi: fine |
CGG AAC CAA ACC CTG AT Agi: C CGG TAC AAA ACC CTA AT new G/C = 44.4%, new Tm = 55.8 added 1 extra base to increase Tm |
bp 5 | bp 236 | VC: SSU rRNA |
| Pink | ttctgcctgacgtagatg Agi: fine |
cctctccggaaccaaac Agi: CCT CTC CGG TAC AAA AC new G/C = 52.9%, new Tm = 55.6 |
bp 12 | bp 226 | VC |
| Yellow | CTGACGTGGATGCTATTC Agi: c ctg acg tag atg cta gtc new G/C = 50%, new Tm = 56.4 - oops, 55.1 added one more "c" at 5' for Tm = 57.7 |
CCGTCAACCGTCACTGTC Agi: fine |
bp 18 | bp 199 | VC small subunit ribosomal RNA gene |
Specificity
| Team Color | Forward primer | Reverse primer | Target site (e.g. bp 60), F | Target side (e.g., bp 300), R | Is bp # for VC or EH? Which gene? |
| Purple | 5' GCG ATG ATT TAG TCT GGC 3' Agi: fine |
5’ CAA TTT CCA ACG ACC ATG C 3’ Agi: fine |
bp 93, F | bp 879, R | VC, SSU rRNA |
| Red | GGT TGA TTC TGC CTG ACG TGG Agi:fine |
CCT TCG TCC TTC ATC ACC ACA A Agi: CCT TCG TCC TTG ATC ACC GAA T (yours doesn't match any known sequence in last 4 bp -- do I have right region?) new G/C = 50%, new Tm = 63.5 |
bp 6, F | bp 588, R | VC, SSU RNA |
| Orange | 5'cgt agt cat aga agg gca aag ag3' Agi: fine |
5' ctc tct ctc tac ctg cta ttg ta 3' Agi: fine |
441 | 1005 | V. corneae TV4/TV5 SSU rRNA |
| Blue | CCGCAATCAGGGACGAA Agi: fine |
GTCAACGTCACTGTCTTGG Agi: GTC AAC C GTC ACT GTC TTG G (insertion) new G/C = 55%, new Tm = 61.8 |
60 | 195 | V. corneae TV4/TV5 SSU rRNA |
