Difference between revisions of "Syntenic dotplot"
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| − | Syntenic dotplot between two '''Escherichia coli''' genomes: B strain REL606 and strain K-12 substrain DH10B. This dotplot was generated using [[SynMap]] can be regenerated [http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=7454;dsgid2=4241;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;dt=geneorder;autogo=1 here]. | + | Syntenic dotplot between two '''Escherichia coli''' genomes: (x-axis) B strain REL606 and (y-axis) strain K-12 substrain DH10B. This dotplot was generated using [[SynMap]] can be regenerated [http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=7454;dsgid2=4241;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;dt=geneorder;autogo=1 here]. |
{| width="1000" cellspacing="1" cellpadding="1" border="1" | {| width="1000" cellspacing="1" cellpadding="1" border="1" | ||
Revision as of 13:39, 6 October 2009
Syntenic dotplot between two Escherichia coli genomes: (x-axis) B strain REL606 and (y-axis) strain K-12 substrain DH10B. This dotplot was generated using SynMap can be regenerated here.
| Variation observed in B and K12 |
Description of variation |
Link leading to GEvo |
| 1. Deletion in B strain |
DNA pol II, genes in metabolic pathway, thiamine ABC transporter present in K12 strain Transposase in K12 strain. Prophage CP46 DNA insertion in K12 strain. |
http://tinyurl.com/yexrzpb |
| 2. Insertions in K12 strain |
Transposase in K12 strain. Prophage CP46 DNA insertion in K12 strain. |
http://tinyurl.com/yd2quy7 |
| 3. Deletion in B strain or Insertion in K12 strain |
Presence of lac operon and other metabolic enzymes genes in K12 strain. Pseudogene made by transposon insertion in K12. | http://tinyurl.com/yedn5tb |
| 4. Insertion in B strain and DNA duplication event in K12. |
Prophage DNA insertion in B strain. Recent DNA duplication event in K12 as seen by 100% identity between paralogs. | http://tinyurl.com/yea8bu6 |
| 5. Insertion in B strain |
Bacteriophage DNA insertion in B strain | http://tinyurl.com/yevlb2w |
| 6. Insertion in B strain |
Prophage DNA insertion in B strain | http://tinyurl.com/ybokuag |
| 7. Insertion in K12 strain |
Prophage DNA insertion in K12 | http://tinyurl.com/yaxlh7o |
| 8. Insertion of transposon in K12 and B strain. Deletion of phenylacetic acid genes in B strain or insertion of those in K12. |
Rac prophage DNA insertion in K12. Insertion of IS3 element protein and transposase in B strain. Insertion of IS30 transposon in B strain created pseudogene. Presence of phenylacetic acid degradation genes in K12 | http://tinyurl.com.ye7wcxe |
| 9. Insertion in K12 strains. Flagella synthesizing genes either deleted in B strain or inserted in K12. |
Presence of flagella encoding/regulatory genes in K12. IS5 sequence insertion in K12. CP4-44 prophage DNA insertion in K12. | http://tinyurl.com/ybh84x7
|
| 10. Insertion in B strain. Pili associated genes and metal resistance genes either inserted in K12 or deleted in B strain. |
Bacteriophage DNA insertion in B strain. IS1 sequence insertion in B strain. Presence of pili associated genes in K12 together with genes conferring resistance to Co and Ni. |
http://tinyurl.com/yammj7v |
| 11. Insertion in K12 strain. ParB family protein and recombinase deleted in K12. |
CP4-57 prophage DNA insertion in K12 strain. Presence of ParB family protein gene and recombinase in B strain |
http://tinyurl.com/ycdog2c |
| 12. Insertion in B and K12 strain. Inversion. Insertion of saframycin synthetase in B strain or deletion of that in K12. |
Prophage DNA insertion in B strain. Inversion of prepilin leader peptidase/methylase and M-type protein. Is5 insertion in K12. Presence of saframycin synthetase gene in B strain.
|
http://tinyurl.com/ycoagxh |
| 13. Insertion of transposon, ShiA-like, TrbC-like proteins in B strain. |
IS30 transposon insertion in B strain. Presence of ShiA-like and TrbC-like protein in B strain |
http://tinyurl.com/ydkrcv8 |
| 14. Insertion in B strain |
Insertion of fimbriae synthesis genes, multi drug transporters, Is1 protein gene in B strain. |
http://tinyurl.com/ycwsmsl |
