Whole genome alighment

[roshanbernard]

Hi,

Can someone suggest me the tools which can be used for whole genome alignments.

I am having the data in contigs and not as one complete circular genome.

and i need to compare two bacteria belong to same species.

can some one help me out

regards

Rosh

[sphil]

there is : Mauve
or this one: MGA

i always used mauve when i had to do a full genome alignment

[roshanbernard]

Thanks a lot for the reply.,

Can i do it even if its a set of contigs. i have around 70 contigs in each genome

[sphil]

Thanks a lot for the reply.,

Can i do it even if its a set of contigs. i have around 70 contigs in each genome

From Mauve docs:

Sequence file input formats

Genome sequence files can be given to Mauve in any of FastA, Multi-FastA, GenBank flat file, or raw formats. Mauve deduces the file format based on the file name extension. By default, a file with any unrecognized file name extension is assumed to be in (Multi-)FastA format.

So I guess that should be no problem!

[roshanbernard]

thank you..