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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
....................

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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