Developing a CONTIG - BAC assembly (Jan/29/2007 )

Hi All,

Could someone in the forum help me. I have three independent BAC sequences which have been generated using shot gun cloning. The sequences have been provided to me in a text file with approximately 30 contigs within each file. The task I would like to perform is to place these contigs in order so that I can create a linearised BAC molecule.

Is there an easy way to do it?. If you need any further information or you think my question is not clear, please do let me know and I can get in touch with you.

Any advice or help will be most appreciated.

thanks and Regards

Raj

-rkota-

What do you mean, "to place these contigs in order" ?

QUOTE (rkota @ Jan 30 2007, 03:44 AM)

The sequences have been provided to me in a text file with approximately 30 contigs within each file.

What is the type/format of that file (file extension)?

I think there was a FASTA splitter available here.

-fedra-

Hi,

All the sequences derived from the shotgun cloning have been placed in one text file (in fasta format). What I need to do is to place these contigs which hopefully have overlaps in a sequential order. For example contig 1 follows 2 so on...

I hope I have made myself clearer.

Thanks and Regards

QUOTE (fedra @ Feb 2 2007, 04:52 AM)

What do you mean, "to place these contigs in order" ?

QUOTE (rkota @ Jan 30 2007, 03:44 AM)

The sequences have been provided to me in a text file with approximately 30 contigs within each file.

What is the type/format of that file (file extension)?

I think there was a FASTA splitter available here.

-rkota-