Genome Comparison

[sushant]

The sequenced data of 3 Pseudomonas strains was obtained from ION torrent and there assembling was done with the help of RAST while there annotation was done with RAST.
I have detected there BGC by uploading the genomes on antiSMASH, my question is now how I can do a further analysis or comparison of the genomes based on the BGC I detected....

Waiting for your suggestions.....

[GenoMax]

I am not familiar with the term BGC (is the bayesian estimation of some kind)?

People generally use Mauve to do genome level comparisons.

[sushant]

Thanks for replying..!!!

BGC stands for Biosynthetic gene clusters.
How could Mauve help me in comparing genomes...? will u please elaborate on this..

[GenoMax]

Did you see/read Mauve web page I linked above?

Do you have an idea of what kind of comparison(s) you want to do (e.g. looking to see what BGC's are conserved in your strains, are there structural rearrangements within the clusters etc)? What is the ultimate aim of your experiment?

[sushant]

The aim of the experiment is...that I have to do a comparative analysis between genomes. So far..I have detected the BGC's from each of the genomes and nw m planning to target a specific BGC so that with the help of its genes I can do some comparative study.
I have read the Mauve web page...if m nt wrng it is a genome alignment tool..which me give me some consensus regions, I hope. Bt what justification will I make if I use Mauve..?

[Bostero]

Good evening

About MAUVE: My question is about the extent or the format of the input files, to make the genome alignment. I haven´t found genomes files of Fusarium oxysporum, in .gb or .gbk format, instead I only found files in .gbff format in GenBank. My question about that is: if I can use those files for alignment (and what to do to load in Mauve without check error), or if you can not use that format, how can I convert or get the files in gb or GBK format.

In advance I appreciate your attention and help. Best

[GenoMax]

Good evening

About MAUVE: My question is about the extent or the format of the input files, to make the genome alignment. I haven´t found genomes files of Fusarium oxysporum, in .gb or .gbk format, instead I only found files in .gbff format in GenBank. My question about that is: if I can use those files for alignment (and what to do to load in Mauve without check error), or if you can not use that format, how can I convert or get the files in gb or GBK format.

In advance I appreciate your attention and help. Best

Mavue can accept fasta/multi-fasta format files in addition to genbank format. So as long as you can find a plain sequence file you should be fine.