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Annotation of GP 84

Original Glimmer call @bp 42099 has strength 10.95
SSC: [start] 42099 [stop] 42617 (fwd direction)
CP:covers all coding potential
SD: 441 (heighest)
SCS: predicted using Glimmer and Genemark
GAP: 4BP overlap
BLAST: 1:1 match Bacillus Phage BigBertha_84
LO: longest
ST:
F: hypothetical protein 916
FS:
ST:

191: Original Glimmer call @bp 124291 has strength 11.73

SSC: 124291 (Start) to 124530 (Stop) FWD

CP: It covers all the coding potential shown on GeneMark.

SD: 819, and it is the highest SD score.

SCS: Predicted by GeneMark and Glimmer.

GAP: overlap (4bp) between start/stop of gp191 and gp190.

BLAST: 1:1 ratio matches with phage BigBertha192.

LO: 246 bp, longest ORF

ST:

F: Low probability range (2.9 ; 3.6); E-value range (2.5E+02 ; 4E+02)

FS: HHpred

ST:

192:Original Glimmer call @bp 124527 has strength 11.01

SSC: 124527 (Start) to 124976 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD: 520, it is not the highest SD score; but it is the highest SD score (546) only has 18bp ORF.

SCS: Predicted by GeneMark and Glimmer.

GAP: Overlap (4bp) between start//stop gp192 and gp191.

BLAST: 1:1 ratio matches with phage Troll.

LO: 450bp, longest ORF.

ST:

F: Low porbability range (6.4 ; 8.6); E-value range (1.4E+02 ; 99) .

FS: HHpred.

ST:

193:Original Glimmer call @bp 124990 has strength 8.23

SSC: 124990 (Start) to 125193 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD: 468, it is not the highest SD score; but it is the highest SD score (546) only has 201bp ORF.

SCS: Predicted by GeneMark and Glimmer.

GAP: Gap (4bp) between start//stop gp194 and gp193.

BLAST:1:1 ratio matches with phage Riley.

LO: 204bp, longest ORF.

ST:

F:

FS:HHpred.

ST:

194:Original Glimmer call @bp 125190 has strength 15.38

SSC: 125190 (Start) to 125453 (Stop) FWD.

CP:It covers all coding potential shown by GeneMark.

SD: 735, it is the highest SD score.

SCS: Predicted by GeneMark and Glimmer.

GAP:Gap (20bp) between start//stop gp195 and gp194.

BLAST: It is not a 1:1 ratio match, but it is a match with phage Troll.

LO:264bp, (318bp) is the longest ORF .

ST:

F:

FS:HHpred.

ST:

195:Original Glimmer call @bp 125474 has strength 15.84

SSC: 125474 (Start) to 125806 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD: 756, it is the highest SD score.

SCS:Predicted by GeneMark and Glimmer.

GAP:Gap (78bp) between start//stop gp196 and gp195.

BLAST: 1:1 ratio matches with phage Troll.

LO:333bp, longest ORF.

ST:

F:

FS:HHpred.

ST:

196:Original Glimmer call @bp 125885 has strength 12.14

SSC:125885 (Start) to 126637 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD:525, it is the highest SD score.

SCS: Predicted by GeneMark and Glimmer.

GAP:Overlap (1bp) between start//stop gp197 and gp196.

BLAST:1:1 ratio matches with phage Troll.

LO:753bp, longest ORF.

ST:

F:

FS:HHpred.

ST:

197:Original Glimmer call @bp 126637 has strength 6.01

SSC:126637 (Start) to 126864 (Stop) FWD.

CP:It covers all coding potential shown by GeneMark.

SD:

SCS: Predicted by GeneMark and Glimmer.

GAP:Overlap (8bp) between start//stop gp192 and gp191.

BLAST: 1:1 ratio matches with phage Troll.

LO:228bp, longest ORF.

ST:

F:

FS:HHpred.

ST:

198:Original Glimmer call @bp 126857 has strength 8.05

SSC: 126857 (Start) to 127405 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD:546, it is the highest SD score.

SCS: Predicted by GeneMark and Glimmer.

GAP:Gap (101bp) between start//stop gp199 and gp198.

BLAST:1:1 ratio matches with phage Riley.

LO:549bp, (567bp) is the longest ORF.

ST:

F:

FS:HHpred.

ST:

199:Original Glimmer call @bp 127507 has strength 13.11

SSC: 127507 (Start) to 128409 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD:546, it is not the highest SD score; but it is the highest SD score (630) only has 825bp ORF.

SCS: Predicted by GeneMark and Glimmer.

GAP:Gap (63bp) between start//stop gp200 and gp199.

BLAST: 1:1 ratio matches with phage Troll.

LO:903bp, longest ORF.

ST:

F:

FS:HHpred.

ST:

200: Original Glimmer call @bp 128473 has strength 8.29

SSC: 128473 (Start) to 128664 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD:546, it is not the highest SD score; but it is the highest SD score (630) only has 135bp ORF.

SCS: Predicted by GeneMark and Glimmer.

GAP:Gap (30bp) between start//stop gp201 and gp200.

BLAST:1:1 ratio matches with phage BigBertha.

LO:192bp, (201bp) is the longest ORF.

ST:

F:

FS:HHpred.

ST:

201: Original GeneMark call @bp 128695

SSC: 128695 (Start) to 128766 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD:924, only SD score available.

SCS: Predicted by GeneMark.

GAP:Overlap (1bp) between start//stop gp202 and gp201.

BLAST:1:1 ratio matches with phage Riley.

LO: 72bp, longest ORF.

ST:

F:

FS:HHpred.

ST:

202: Original Glimmer call @bp 128768 has strength 5.19

SSC: 128768 (Start) to 128953 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD:504, it is the highest SD score; there are two SD score of 504, but with different ORF lengths.

SCS: Predicted by GeneMark and Glimmer.

GAP:Overlap (2bp) between start//stop gp203 and gp202.

BLAST: 1:1 ratio matches with phage Troll.

LO:168bp, longest ORF.

ST:

F:

FS:HHpred.

ST:

203: Original Glimmer call @bp 128946 has strength 13.56

SSC: 128946 (Start) to 129296 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD:567, it is the highest SD score.

SCS: Predicted by GeneMark and Glimmer.

GAP:Gap (348bp) between start//stop gp204 and gp203.

BLAST:1:1 ratio matches with BTP 29.

LO:351bp, longest ORF.

ST:

F:

FS:HHpred.

ST:

204: Original Glimmer call @bp 129301 has strength 5.82 ** not called by GeneMark

SSC: 129301 (Start) to 129420 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD: 345, it is not the highest SD score; but it is the highest SD score (399) only has 33bp ORF.

SCS: Predicted by GeneMark and Glimmer.

GAP:Gap (137bp) between start//stop gp205 and gp204.

BLAST:1:1 ratio matches with phage BigBertha 206.  

LO: 138bp, longest ORF.

ST:

F:

FS:HHpred.

ST:

205:Original Glimmer call @bp 129433 has strength 6.52

SSC: 129433 (Start) to 129636 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD: 819, it is the highest SD score; but it is the highest SD score which has 201bp ORF, which is shorter than the SD (441) with 204bp ORF.

SCS:Predicted by GeneMark and Glimmer.

GAP:Overlap (8bp) between start//stop gp206 and gp205.

BLAST:1:1 ratio matches with phage BigBertha 207.

LO:201bp, (204bp) is the longest ORF.

ST:

F:

FS:HHpred.

ST:

206: Original Glimmer call @bp 129629 has strength 6.30

SSC: 129629 (Start) to 129892 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD:630, it is the highest SD score.

SCS: Predicted by GeneMark and Glimmer.

GAP:Gap (16bp) between start//stop gp207 and gp206.

BLAST:1:1 ratio matches with phage BigBertha 208.

LO:264bp, longest ORF.

ST:

F:

FS:HHpred.

ST:

207: Original Glimmer call @bp 129877 has strength 5.55

SSC: 129877 (Start) to 130593 (Stop) FWD.

CP: It covers all coding potential shown by GeneMark.

SD: 357, it is the highest SD score; but it is the highest SD score which has 717bp ORF, which is shorter than the SD (336) with 756bp ORF.

SCS: Predicted by GeneMark and Glimmer.

GAP:

BLAST: 1:1 ratio matches with phage BigBertha.

LO:717bp, (756bp) is the longest ORF.

ST:

F:

FS:HHpred.

ST:

Original Glimmer call @bp 1184 has strength 15.18

SSC: start 1181, stop 1684

CP: includes all coding potential

SD: score is 735 and it is the highest

SCS: predicted by G and GM

GAP: no 5' gene, first gene

BLAST: 1:1 macthes to gp61 of phage4

LO: longest open reading frame

ST:

F:

FS: Pharmerator, blastp

ST:

TEST

OH NO CONSED HAS CRASHEDDDDDDDDD

Phage Lab...Round 4!

This year will be my 4th round of Phage Lab! Are you as excited as I am?! 

- Rachel

P.S. We did have blogs when I was in high school... ;)

This is a blog post

When I was in highschool, blogs didn't exist.