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Annotation of assembled genomes:
Using sequences of aligned parts of both genomes we run Fgenesb gene
annotation pipeline on both sequences. Two fragments of the annotation
is presented below (The first is for TAG11 contig assembled from short
reads and the second is for AV19 sequence. We can see that pipeline predicted
almost the same genes in both genomes (while they have small differences in their length).
Prediction of potential genes in microbial genomes
Time: Tue Nov 13 12:41:03 2007
Seq name: contig of TAG11 length:31967
Length of sequence - 31967 bp
Number of predicted genes - 41, with homology - 34
Number of transcription units - 16, operones - 9 average op.length - 3.8
N Tu/Op Conserved S Start End Score
pairs(N/Pv)
1 1 Op 1 . - CDS 3 - 1353 391 ## COG0144 tRNA and rRNA cytosine-C5-methylases
2 1 Op 2 . - CDS 1310 - 1534 112 ##
+ Prom 1499 - 1558 2.6
3 2 Tu 1 1/0.667 + CDS 1622 - 2263 471 ## COG4034 Uncharacterized protein conserved in
4 3 Tu 1 . + CDS 2397 - 3242 516 ## COG0157 Nicotinate-nucleotide pyrophosphoryl
5 4 Op 1 . - CDS 3264 - 4277 567 ##
6 4 Op 2 . - CDS 4217 - 4711 247 ## COG0028 Thiamine pyrophosphate-requiring enz
7 4 Op 3 . - CDS 4728 - 5096 234 ##
8 5 Tu 1 . + CDS 5218 - 5730 220 ## COG1813 Predicted transcription factor, homo
9 6 Op 1 . - CDS 5734 - 6363 283 ##
10 6 Op 2 1/0.667 - CDS 6293 - 7843 740 ## COG0849 Actin-like ATPase involved in cell d
11 6 Op 3 2/0.000 - CDS 7923 - 8234 146 ## COG1694 Predicted pyrophosphatase
12 6 Op 4 . - CDS 8231 - 8779 212 ## COG0500 SAM-dependent methyltransferases
+ Prom 9049 - 9108 2.8
13 7 Op 1 2/0.000 + CDS 9262 - 9609 267 ## COG4921 Uncharacterized protein conserved in
14 7 Op 2 . + CDS 9614 - 10849 686 ## COG2262 GTPase
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Prediction of potential genes in microbial genomes
Time: Tue Nov 13 12:36:21 2007
Seq name: gi|20093440|ref|NC_003551.1| Methanopyrus kandleri AV19, complete genome 414494 447500
Length of sequence - 33007 bp
Number of predicted genes - 44, with homology - 34
Number of transcription units - 17, operones - 10 average op.length - 3.7
N Tu/Op Conserved S Start End Score
pairs(N/Pv)
1 1 Op 1 . - CDS 3 - 1248 606 ## COG0144 tRNA and rRNA cytosine-C5-methylases
2 1 Op 2 . - CDS 1289 - 1540 146 ##
3 2 Tu 1 1/0.667 + CDS 1643 - 2269 431 ## COG4034 Uncharacterized protein conserved in
+ Prom 2282 - 2341 2.1
4 3 Tu 1 . + CDS 2420 - 3268 493 ## COG0157 Nicotinate-nucleotide pyrophosphoryl
5 4 Op 1 . - CDS 3286 - 4299 640 ##
6 4 Op 2 . - CDS 4239 - 4676 272 ## COG0028 Thiamine pyrophosphate-requiring enz
7 4 Op 3 . - CDS 4750 - 5118 238 ##
8 5 Tu 1 . + CDS 5240 - 5755 212 ## COG1813 Predicted transcription factor, homo
9 6 Op 1 . - CDS 5759 - 6391 347 ##
10 6 Op 2 1/0.667 - CDS 6321 - 7871 640 ## COG0849 Actin-like ATPase involved in cell d
11 6 Op 3 2/0.000 - CDS 7951 - 8262 149 ## COG1694 Predicted pyrophosphatase
12 6 Op 4 . - CDS 8259 - 8807 234 ## COG0500 SAM-dependent methyltransferases
+ Prom 9077 - 9136 2.8
13 7 Op 1 2/0.000 + CDS 9290 - 9637 273 ## COG4921 Uncharacterized protein conserved in
14 7 Op 2 . + CDS 9642 - 10877 690 ## COG2262 GTPases
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